Starting phenix.real_space_refine on Sun Sep 29 21:55:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwb_10037/09_2024/6rwb_10037.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwb_10037/09_2024/6rwb_10037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwb_10037/09_2024/6rwb_10037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwb_10037/09_2024/6rwb_10037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwb_10037/09_2024/6rwb_10037.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwb_10037/09_2024/6rwb_10037.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 47760 2.51 5 N 12855 2.21 5 O 14595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 75405 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 15081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1873, 15081 Classifications: {'peptide': 1873} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 59, 'TRANS': 1813} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: C, B, E, D Time building chain proxies: 43.06, per 1000 atoms: 0.57 Number of scatterers: 75405 At special positions: 0 Unit cell: (163.2, 160.48, 257.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 14595 8.00 N 12855 7.00 C 47760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.30 Conformation dependent library (CDL) restraints added in 7.4 seconds 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17900 Finding SS restraints... Secondary structure from input PDB file: 310 helices and 55 sheets defined 53.8% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.16 Creating SS restraints... Processing helix chain 'A' and resid 58 through 68 removed outlier: 3.528A pdb=" N LEU A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Proline residue: A 64 - end of helix removed outlier: 3.537A pdb=" N THR A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.761A pdb=" N LEU A 128 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 143 through 153 removed outlier: 3.844A pdb=" N LYS A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.840A pdb=" N THR A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.983A pdb=" N PHE A 171 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR A 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 172' Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.635A pdb=" N THR A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 removed outlier: 3.580A pdb=" N LEU A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.727A pdb=" N GLN A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 248 through 262 removed outlier: 3.726A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 260 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 288 removed outlier: 3.576A pdb=" N ILE A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.363A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 372 through 387 removed outlier: 3.638A pdb=" N GLN A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.578A pdb=" N LEU A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 401 removed outlier: 3.681A pdb=" N TYR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 removed outlier: 3.698A pdb=" N LYS A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 437 removed outlier: 3.511A pdb=" N ILE A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 457 through 470 removed outlier: 3.935A pdb=" N ASN A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 492 removed outlier: 4.021A pdb=" N ASN A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 507 removed outlier: 3.715A pdb=" N ASN A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 525 removed outlier: 3.769A pdb=" N THR A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 Processing helix chain 'A' and resid 538 through 558 removed outlier: 4.003A pdb=" N LEU A 542 " --> pdb=" O HIS A 538 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 569 removed outlier: 3.504A pdb=" N ILE A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 601 removed outlier: 3.984A pdb=" N SER A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 601 " --> pdb=" O CYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 removed outlier: 3.623A pdb=" N LEU A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 661 removed outlier: 3.557A pdb=" N GLU A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 646 " --> pdb=" O GLY A 642 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 708 removed outlier: 4.051A pdb=" N LEU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 685 " --> pdb=" O ASN A 681 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 708 " --> pdb=" O LYS A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 726 removed outlier: 3.625A pdb=" N ILE A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.781A pdb=" N PHE A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.689A pdb=" N ASN A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 removed outlier: 3.844A pdb=" N ILE A 806 " --> pdb=" O HIS A 802 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE A 807 " --> pdb=" O PRO A 803 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 828 removed outlier: 3.817A pdb=" N ASN A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 858 removed outlier: 3.594A pdb=" N ASP A 849 " --> pdb=" O GLU A 845 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 853 " --> pdb=" O ASP A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 877 Processing helix chain 'A' and resid 889 through 907 removed outlier: 3.729A pdb=" N ASP A 907 " --> pdb=" O ASN A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 922 removed outlier: 3.711A pdb=" N ILE A 918 " --> pdb=" O HIS A 914 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR A 920 " --> pdb=" O LYS A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 948 Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 980 through 999 removed outlier: 3.875A pdb=" N VAL A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 998 " --> pdb=" O SER A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1276 removed outlier: 3.685A pdb=" N GLN A1276 " --> pdb=" O VAL A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1290 removed outlier: 4.151A pdb=" N ASP A1290 " --> pdb=" O SER A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1323 removed outlier: 3.740A pdb=" N PHE A1305 " --> pdb=" O TYR A1301 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE A1312 " --> pdb=" O PHE A1308 " (cutoff:3.500A) Proline residue: A1313 - end of helix removed outlier: 3.619A pdb=" N ARG A1319 " --> pdb=" O LEU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1334 removed outlier: 4.028A pdb=" N HIS A1331 " --> pdb=" O ASP A1327 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP A1332 " --> pdb=" O LEU A1328 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A1333 " --> pdb=" O ALA A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1389 removed outlier: 3.731A pdb=" N ILE A1385 " --> pdb=" O ASP A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1412 removed outlier: 3.531A pdb=" N PHE A1398 " --> pdb=" O LYS A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1436 removed outlier: 3.939A pdb=" N ILE A1426 " --> pdb=" O ALA A1422 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR A1427 " --> pdb=" O GLU A1423 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A1428 " --> pdb=" O ALA A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1487 removed outlier: 3.911A pdb=" N TRP A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A1477 " --> pdb=" O LEU A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1624 removed outlier: 3.591A pdb=" N LEU A1540 " --> pdb=" O ARG A1536 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER A1546 " --> pdb=" O GLU A1542 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP A1566 " --> pdb=" O LEU A1562 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A1583 " --> pdb=" O GLN A1579 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS A1586 " --> pdb=" O LEU A1582 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A1593 " --> pdb=" O GLN A1589 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A1594 " --> pdb=" O ASN A1590 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A1596 " --> pdb=" O ASN A1592 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A1601 " --> pdb=" O GLN A1597 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A1605 " --> pdb=" O GLU A1601 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A1606 " --> pdb=" O ALA A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1644 removed outlier: 3.947A pdb=" N ARG A1636 " --> pdb=" O GLY A1632 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A1637 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A1642 " --> pdb=" O ASP A1638 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A1644 " --> pdb=" O GLY A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1658 removed outlier: 3.686A pdb=" N THR A1658 " --> pdb=" O ALA A1654 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1761 removed outlier: 3.849A pdb=" N HIS A1726 " --> pdb=" O GLU A1722 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A1743 " --> pdb=" O GLN A1739 " (cutoff:3.500A) Processing helix chain 'A' and resid 1765 through 1802 removed outlier: 3.813A pdb=" N TRP A1771 " --> pdb=" O GLU A1767 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY A1778 " --> pdb=" O GLY A1774 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A1781 " --> pdb=" O SER A1777 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A1782 " --> pdb=" O GLY A1778 " (cutoff:3.500A) Proline residue: A1789 - end of helix removed outlier: 4.031A pdb=" N LYS A1800 " --> pdb=" O ALA A1796 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU A1801 " --> pdb=" O VAL A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1843 removed outlier: 3.944A pdb=" N ASP A1828 " --> pdb=" O LEU A1824 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A1829 " --> pdb=" O ALA A1825 " (cutoff:3.500A) Processing helix chain 'A' and resid 1869 through 1878 Processing helix chain 'A' and resid 1907 through 1910 Processing helix chain 'B' and resid 59 through 68 Proline residue: B 64 - end of helix removed outlier: 3.537A pdb=" N THR B 68 " --> pdb=" O PRO B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.760A pdb=" N LEU B 128 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 143 through 153 removed outlier: 3.845A pdb=" N LYS B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 removed outlier: 3.840A pdb=" N THR B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.983A pdb=" N PHE B 171 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 168 through 172' Processing helix chain 'B' and resid 176 through 189 removed outlier: 3.636A pdb=" N THR B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 199 removed outlier: 3.579A pdb=" N LEU B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.726A pdb=" N GLN B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 248 through 262 removed outlier: 3.725A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 260 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 288 removed outlier: 3.577A pdb=" N ILE B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 313 through 319 Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.364A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 372 through 387 removed outlier: 3.639A pdb=" N GLN B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 383 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Proline residue: B 384 - end of helix removed outlier: 3.578A pdb=" N LEU B 387 " --> pdb=" O ILE B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 401 removed outlier: 3.681A pdb=" N TYR B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.699A pdb=" N LYS B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 437 removed outlier: 3.512A pdb=" N ILE B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 457 through 470 removed outlier: 3.934A pdb=" N ASN B 466 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 492 removed outlier: 4.021A pdb=" N ASN B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 507 removed outlier: 3.715A pdb=" N ASN B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 525 removed outlier: 3.768A pdb=" N THR B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 538 Processing helix chain 'B' and resid 538 through 558 removed outlier: 4.003A pdb=" N LEU B 542 " --> pdb=" O HIS B 538 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 551 " --> pdb=" O LYS B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 569 removed outlier: 3.504A pdb=" N ILE B 565 " --> pdb=" O SER B 561 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 601 removed outlier: 3.984A pdb=" N SER B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 601 " --> pdb=" O CYS B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 617 removed outlier: 3.624A pdb=" N LEU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 661 removed outlier: 3.557A pdb=" N GLU B 624 " --> pdb=" O ASN B 620 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B 646 " --> pdb=" O GLY B 642 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 647 " --> pdb=" O SER B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 708 removed outlier: 4.051A pdb=" N LEU B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 685 " --> pdb=" O ASN B 681 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 695 " --> pdb=" O GLY B 691 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 726 removed outlier: 3.626A pdb=" N ILE B 720 " --> pdb=" O SER B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.780A pdb=" N PHE B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 799 removed outlier: 3.689A pdb=" N ASN B 791 " --> pdb=" O LEU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 815 removed outlier: 3.844A pdb=" N ILE B 806 " --> pdb=" O HIS B 802 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 807 " --> pdb=" O PRO B 803 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 828 removed outlier: 3.817A pdb=" N ASN B 826 " --> pdb=" O GLU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 858 removed outlier: 3.595A pdb=" N ASP B 849 " --> pdb=" O GLU B 845 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 850 " --> pdb=" O SER B 846 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 853 " --> pdb=" O ASP B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 877 Processing helix chain 'B' and resid 889 through 907 removed outlier: 3.727A pdb=" N ASP B 907 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 922 removed outlier: 3.712A pdb=" N ILE B 918 " --> pdb=" O HIS B 914 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR B 920 " --> pdb=" O LYS B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 948 Processing helix chain 'B' and resid 964 through 972 Processing helix chain 'B' and resid 980 through 999 removed outlier: 3.875A pdb=" N VAL B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 998 " --> pdb=" O SER B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1268 through 1276 removed outlier: 3.685A pdb=" N GLN B1276 " --> pdb=" O VAL B1272 " (cutoff:3.500A) Processing helix chain 'B' and resid 1284 through 1290 removed outlier: 4.152A pdb=" N ASP B1290 " --> pdb=" O SER B1286 " (cutoff:3.500A) Processing helix chain 'B' and resid 1301 through 1323 removed outlier: 3.740A pdb=" N PHE B1305 " --> pdb=" O TYR B1301 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE B1312 " --> pdb=" O PHE B1308 " (cutoff:3.500A) Proline residue: B1313 - end of helix removed outlier: 3.619A pdb=" N ARG B1319 " --> pdb=" O LEU B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1325 through 1334 removed outlier: 4.027A pdb=" N HIS B1331 " --> pdb=" O ASP B1327 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP B1332 " --> pdb=" O LEU B1328 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B1333 " --> pdb=" O ALA B1329 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1389 removed outlier: 3.731A pdb=" N ILE B1385 " --> pdb=" O ASP B1381 " (cutoff:3.500A) Processing helix chain 'B' and resid 1390 through 1412 removed outlier: 3.530A pdb=" N PHE B1398 " --> pdb=" O LYS B1394 " (cutoff:3.500A) Processing helix chain 'B' and resid 1417 through 1436 removed outlier: 3.939A pdb=" N ILE B1426 " --> pdb=" O ALA B1422 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR B1427 " --> pdb=" O GLU B1423 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR B1428 " --> pdb=" O ALA B1424 " (cutoff:3.500A) Processing helix chain 'B' and resid 1470 through 1487 removed outlier: 3.911A pdb=" N TRP B1476 " --> pdb=" O LEU B1472 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP B1477 " --> pdb=" O LEU B1473 " (cutoff:3.500A) Processing helix chain 'B' and resid 1536 through 1624 removed outlier: 3.592A pdb=" N LEU B1540 " --> pdb=" O ARG B1536 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER B1546 " --> pdb=" O GLU B1542 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP B1566 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B1583 " --> pdb=" O GLN B1579 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B1586 " --> pdb=" O LEU B1582 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B1593 " --> pdb=" O GLN B1589 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B1594 " --> pdb=" O ASN B1590 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B1596 " --> pdb=" O ASN B1592 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B1601 " --> pdb=" O GLN B1597 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B1605 " --> pdb=" O GLU B1601 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B1606 " --> pdb=" O ALA B1602 " (cutoff:3.500A) Processing helix chain 'B' and resid 1626 through 1644 removed outlier: 3.946A pdb=" N ARG B1636 " --> pdb=" O GLY B1632 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B1637 " --> pdb=" O LEU B1633 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B1642 " --> pdb=" O ASP B1638 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B1644 " --> pdb=" O GLY B1640 " (cutoff:3.500A) Processing helix chain 'B' and resid 1647 through 1658 removed outlier: 3.686A pdb=" N THR B1658 " --> pdb=" O ALA B1654 " (cutoff:3.500A) Processing helix chain 'B' and resid 1673 through 1761 removed outlier: 3.850A pdb=" N HIS B1726 " --> pdb=" O GLU B1722 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B1743 " --> pdb=" O GLN B1739 " (cutoff:3.500A) Processing helix chain 'B' and resid 1765 through 1802 removed outlier: 3.813A pdb=" N TRP B1771 " --> pdb=" O GLU B1767 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY B1778 " --> pdb=" O GLY B1774 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B1781 " --> pdb=" O SER B1777 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B1782 " --> pdb=" O GLY B1778 " (cutoff:3.500A) Proline residue: B1789 - end of helix removed outlier: 4.031A pdb=" N LYS B1800 " --> pdb=" O ALA B1796 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU B1801 " --> pdb=" O VAL B1797 " (cutoff:3.500A) Processing helix chain 'B' and resid 1824 through 1843 removed outlier: 3.944A pdb=" N ASP B1828 " --> pdb=" O LEU B1824 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B1829 " --> pdb=" O ALA B1825 " (cutoff:3.500A) Processing helix chain 'B' and resid 1869 through 1878 Processing helix chain 'B' and resid 1907 through 1910 Processing helix chain 'C' and resid 59 through 68 Proline residue: C 64 - end of helix removed outlier: 3.537A pdb=" N THR C 68 " --> pdb=" O PRO C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 107 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 124 through 128 removed outlier: 3.760A pdb=" N LEU C 128 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 137 Processing helix chain 'C' and resid 143 through 153 removed outlier: 3.844A pdb=" N LYS C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 161 removed outlier: 3.840A pdb=" N THR C 159 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.983A pdb=" N PHE C 171 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR C 172 " --> pdb=" O SER C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 172' Processing helix chain 'C' and resid 176 through 189 removed outlier: 3.636A pdb=" N THR C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.579A pdb=" N LEU C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.727A pdb=" N GLN C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 245 Processing helix chain 'C' and resid 248 through 262 removed outlier: 3.726A pdb=" N LEU C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 260 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 288 removed outlier: 3.577A pdb=" N ILE C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 Processing helix chain 'C' and resid 313 through 319 Processing helix chain 'C' and resid 335 through 345 removed outlier: 4.363A pdb=" N ILE C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 Processing helix chain 'C' and resid 372 through 387 removed outlier: 3.639A pdb=" N GLN C 376 " --> pdb=" O LYS C 372 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET C 380 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 383 " --> pdb=" O ARG C 379 " (cutoff:3.500A) Proline residue: C 384 - end of helix removed outlier: 3.579A pdb=" N LEU C 387 " --> pdb=" O ILE C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 401 removed outlier: 3.681A pdb=" N TYR C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 414 removed outlier: 3.699A pdb=" N LYS C 411 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 437 removed outlier: 3.512A pdb=" N ILE C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN C 437 " --> pdb=" O TRP C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 457 through 470 removed outlier: 3.934A pdb=" N ASN C 466 " --> pdb=" O ASN C 462 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 492 removed outlier: 4.020A pdb=" N ASN C 483 " --> pdb=" O SER C 479 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 507 removed outlier: 3.715A pdb=" N ASN C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 525 removed outlier: 3.768A pdb=" N THR C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 538 through 558 removed outlier: 4.003A pdb=" N LEU C 542 " --> pdb=" O HIS C 538 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 551 " --> pdb=" O LYS C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 569 removed outlier: 3.505A pdb=" N ILE C 565 " --> pdb=" O SER C 561 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 568 " --> pdb=" O GLU C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 601 removed outlier: 3.984A pdb=" N SER C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 601 " --> pdb=" O CYS C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 617 removed outlier: 3.623A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 661 removed outlier: 3.558A pdb=" N GLU C 624 " --> pdb=" O ASN C 620 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 633 " --> pdb=" O SER C 629 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN C 646 " --> pdb=" O GLY C 642 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER C 647 " --> pdb=" O SER C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 708 removed outlier: 4.052A pdb=" N LEU C 682 " --> pdb=" O GLU C 678 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 684 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 685 " --> pdb=" O ASN C 681 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU C 695 " --> pdb=" O GLY C 691 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN C 708 " --> pdb=" O LYS C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 726 removed outlier: 3.626A pdb=" N ILE C 720 " --> pdb=" O SER C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 742 removed outlier: 3.780A pdb=" N PHE C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 799 removed outlier: 3.689A pdb=" N ASN C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 815 removed outlier: 3.843A pdb=" N ILE C 806 " --> pdb=" O HIS C 802 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE C 807 " --> pdb=" O PRO C 803 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 828 removed outlier: 3.817A pdb=" N ASN C 826 " --> pdb=" O GLU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 858 removed outlier: 3.595A pdb=" N ASP C 849 " --> pdb=" O GLU C 845 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C 850 " --> pdb=" O SER C 846 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN C 853 " --> pdb=" O ASP C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 877 Processing helix chain 'C' and resid 889 through 907 removed outlier: 3.729A pdb=" N ASP C 907 " --> pdb=" O ASN C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 922 removed outlier: 3.711A pdb=" N ILE C 918 " --> pdb=" O HIS C 914 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR C 920 " --> pdb=" O LYS C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 948 Processing helix chain 'C' and resid 964 through 972 Processing helix chain 'C' and resid 980 through 999 removed outlier: 3.875A pdb=" N VAL C 984 " --> pdb=" O THR C 980 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS C 997 " --> pdb=" O ILE C 993 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 998 " --> pdb=" O SER C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1268 through 1276 removed outlier: 3.685A pdb=" N GLN C1276 " --> pdb=" O VAL C1272 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1290 removed outlier: 4.151A pdb=" N ASP C1290 " --> pdb=" O SER C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1301 through 1323 removed outlier: 3.740A pdb=" N PHE C1305 " --> pdb=" O TYR C1301 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE C1312 " --> pdb=" O PHE C1308 " (cutoff:3.500A) Proline residue: C1313 - end of helix removed outlier: 3.619A pdb=" N ARG C1319 " --> pdb=" O LEU C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1325 through 1334 removed outlier: 4.027A pdb=" N HIS C1331 " --> pdb=" O ASP C1327 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP C1332 " --> pdb=" O LEU C1328 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C1333 " --> pdb=" O ALA C1329 " (cutoff:3.500A) Processing helix chain 'C' and resid 1381 through 1389 removed outlier: 3.731A pdb=" N ILE C1385 " --> pdb=" O ASP C1381 " (cutoff:3.500A) Processing helix chain 'C' and resid 1390 through 1412 removed outlier: 3.530A pdb=" N PHE C1398 " --> pdb=" O LYS C1394 " (cutoff:3.500A) Processing helix chain 'C' and resid 1417 through 1436 removed outlier: 3.939A pdb=" N ILE C1426 " --> pdb=" O ALA C1422 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR C1427 " --> pdb=" O GLU C1423 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR C1428 " --> pdb=" O ALA C1424 " (cutoff:3.500A) Processing helix chain 'C' and resid 1470 through 1487 removed outlier: 3.911A pdb=" N TRP C1476 " --> pdb=" O LEU C1472 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP C1477 " --> pdb=" O LEU C1473 " (cutoff:3.500A) Processing helix chain 'C' and resid 1536 through 1624 removed outlier: 3.591A pdb=" N LEU C1540 " --> pdb=" O ARG C1536 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER C1546 " --> pdb=" O GLU C1542 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP C1566 " --> pdb=" O LEU C1562 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C1583 " --> pdb=" O GLN C1579 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS C1586 " --> pdb=" O LEU C1582 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C1593 " --> pdb=" O GLN C1589 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C1594 " --> pdb=" O ASN C1590 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C1596 " --> pdb=" O ASN C1592 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C1601 " --> pdb=" O GLN C1597 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C1605 " --> pdb=" O GLU C1601 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU C1606 " --> pdb=" O ALA C1602 " (cutoff:3.500A) Processing helix chain 'C' and resid 1626 through 1644 removed outlier: 3.947A pdb=" N ARG C1636 " --> pdb=" O GLY C1632 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE C1637 " --> pdb=" O LEU C1633 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C1642 " --> pdb=" O ASP C1638 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C1644 " --> pdb=" O GLY C1640 " (cutoff:3.500A) Processing helix chain 'C' and resid 1647 through 1658 removed outlier: 3.686A pdb=" N THR C1658 " --> pdb=" O ALA C1654 " (cutoff:3.500A) Processing helix chain 'C' and resid 1673 through 1761 removed outlier: 3.850A pdb=" N HIS C1726 " --> pdb=" O GLU C1722 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN C1743 " --> pdb=" O GLN C1739 " (cutoff:3.500A) Processing helix chain 'C' and resid 1765 through 1802 removed outlier: 3.814A pdb=" N TRP C1771 " --> pdb=" O GLU C1767 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY C1778 " --> pdb=" O GLY C1774 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE C1781 " --> pdb=" O SER C1777 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN C1782 " --> pdb=" O GLY C1778 " (cutoff:3.500A) Proline residue: C1789 - end of helix removed outlier: 4.031A pdb=" N LYS C1800 " --> pdb=" O ALA C1796 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU C1801 " --> pdb=" O VAL C1797 " (cutoff:3.500A) Processing helix chain 'C' and resid 1824 through 1843 removed outlier: 3.944A pdb=" N ASP C1828 " --> pdb=" O LEU C1824 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C1829 " --> pdb=" O ALA C1825 " (cutoff:3.500A) Processing helix chain 'C' and resid 1869 through 1878 Processing helix chain 'C' and resid 1907 through 1910 Processing helix chain 'D' and resid 59 through 68 Proline residue: D 64 - end of helix removed outlier: 3.537A pdb=" N THR D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 107 Processing helix chain 'D' and resid 117 through 122 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.762A pdb=" N LEU D 128 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 143 through 153 removed outlier: 3.845A pdb=" N LYS D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.840A pdb=" N THR D 159 " --> pdb=" O LEU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.983A pdb=" N PHE D 171 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR D 172 " --> pdb=" O SER D 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 168 through 172' Processing helix chain 'D' and resid 176 through 189 removed outlier: 3.636A pdb=" N THR D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS D 189 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.580A pdb=" N LEU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 removed outlier: 3.726A pdb=" N GLN D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 245 Processing helix chain 'D' and resid 248 through 262 removed outlier: 3.726A pdb=" N LEU D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 260 " --> pdb=" O ASN D 256 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 288 removed outlier: 3.576A pdb=" N ILE D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 Processing helix chain 'D' and resid 313 through 319 Processing helix chain 'D' and resid 335 through 345 removed outlier: 4.364A pdb=" N ILE D 339 " --> pdb=" O SER D 335 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 357 Processing helix chain 'D' and resid 372 through 387 removed outlier: 3.639A pdb=" N GLN D 376 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET D 380 " --> pdb=" O GLN D 376 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 383 " --> pdb=" O ARG D 379 " (cutoff:3.500A) Proline residue: D 384 - end of helix removed outlier: 3.578A pdb=" N LEU D 387 " --> pdb=" O ILE D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 401 removed outlier: 3.681A pdb=" N TYR D 401 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 414 removed outlier: 3.697A pdb=" N LYS D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 437 removed outlier: 3.513A pdb=" N ILE D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 424 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN D 437 " --> pdb=" O TRP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 457 through 470 removed outlier: 3.935A pdb=" N ASN D 466 " --> pdb=" O ASN D 462 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 492 removed outlier: 4.021A pdb=" N ASN D 483 " --> pdb=" O SER D 479 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 507 removed outlier: 3.715A pdb=" N ASN D 504 " --> pdb=" O ALA D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 525 removed outlier: 3.769A pdb=" N THR D 525 " --> pdb=" O ASN D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 538 Processing helix chain 'D' and resid 538 through 558 removed outlier: 4.003A pdb=" N LEU D 542 " --> pdb=" O HIS D 538 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D 551 " --> pdb=" O LYS D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 569 removed outlier: 3.505A pdb=" N ILE D 565 " --> pdb=" O SER D 561 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 601 removed outlier: 3.983A pdb=" N SER D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 601 " --> pdb=" O CYS D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 617 removed outlier: 3.624A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 661 removed outlier: 3.558A pdb=" N GLU D 624 " --> pdb=" O ASN D 620 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 633 " --> pdb=" O SER D 629 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN D 646 " --> pdb=" O GLY D 642 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER D 647 " --> pdb=" O SER D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 708 removed outlier: 4.052A pdb=" N LEU D 682 " --> pdb=" O GLU D 678 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS D 684 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER D 685 " --> pdb=" O ASN D 681 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 695 " --> pdb=" O GLY D 691 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 726 removed outlier: 3.625A pdb=" N ILE D 720 " --> pdb=" O SER D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 removed outlier: 3.780A pdb=" N PHE D 737 " --> pdb=" O ALA D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 799 removed outlier: 3.689A pdb=" N ASN D 791 " --> pdb=" O LEU D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 815 removed outlier: 3.843A pdb=" N ILE D 806 " --> pdb=" O HIS D 802 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE D 807 " --> pdb=" O PRO D 803 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 828 removed outlier: 3.817A pdb=" N ASN D 826 " --> pdb=" O GLU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 858 removed outlier: 3.594A pdb=" N ASP D 849 " --> pdb=" O GLU D 845 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 850 " --> pdb=" O SER D 846 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN D 853 " --> pdb=" O ASP D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 877 Processing helix chain 'D' and resid 889 through 907 removed outlier: 3.728A pdb=" N ASP D 907 " --> pdb=" O ASN D 903 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 922 removed outlier: 3.711A pdb=" N ILE D 918 " --> pdb=" O HIS D 914 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR D 920 " --> pdb=" O LYS D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 948 Processing helix chain 'D' and resid 964 through 972 Processing helix chain 'D' and resid 980 through 999 removed outlier: 3.875A pdb=" N VAL D 984 " --> pdb=" O THR D 980 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 998 " --> pdb=" O SER D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1268 through 1276 removed outlier: 3.685A pdb=" N GLN D1276 " --> pdb=" O VAL D1272 " (cutoff:3.500A) Processing helix chain 'D' and resid 1284 through 1290 removed outlier: 4.152A pdb=" N ASP D1290 " --> pdb=" O SER D1286 " (cutoff:3.500A) Processing helix chain 'D' and resid 1301 through 1323 removed outlier: 3.740A pdb=" N PHE D1305 " --> pdb=" O TYR D1301 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE D1312 " --> pdb=" O PHE D1308 " (cutoff:3.500A) Proline residue: D1313 - end of helix removed outlier: 3.619A pdb=" N ARG D1319 " --> pdb=" O LEU D1315 " (cutoff:3.500A) Processing helix chain 'D' and resid 1325 through 1334 removed outlier: 4.027A pdb=" N HIS D1331 " --> pdb=" O ASP D1327 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP D1332 " --> pdb=" O LEU D1328 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D1333 " --> pdb=" O ALA D1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 1381 through 1389 removed outlier: 3.730A pdb=" N ILE D1385 " --> pdb=" O ASP D1381 " (cutoff:3.500A) Processing helix chain 'D' and resid 1390 through 1412 removed outlier: 3.531A pdb=" N PHE D1398 " --> pdb=" O LYS D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1417 through 1436 removed outlier: 3.939A pdb=" N ILE D1426 " --> pdb=" O ALA D1422 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR D1427 " --> pdb=" O GLU D1423 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR D1428 " --> pdb=" O ALA D1424 " (cutoff:3.500A) Processing helix chain 'D' and resid 1470 through 1487 removed outlier: 3.910A pdb=" N TRP D1476 " --> pdb=" O LEU D1472 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP D1477 " --> pdb=" O LEU D1473 " (cutoff:3.500A) Processing helix chain 'D' and resid 1536 through 1624 removed outlier: 3.592A pdb=" N LEU D1540 " --> pdb=" O ARG D1536 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER D1546 " --> pdb=" O GLU D1542 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP D1566 " --> pdb=" O LEU D1562 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN D1583 " --> pdb=" O GLN D1579 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS D1586 " --> pdb=" O LEU D1582 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D1593 " --> pdb=" O GLN D1589 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN D1594 " --> pdb=" O ASN D1590 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D1596 " --> pdb=" O ASN D1592 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D1601 " --> pdb=" O GLN D1597 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER D1605 " --> pdb=" O GLU D1601 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D1606 " --> pdb=" O ALA D1602 " (cutoff:3.500A) Processing helix chain 'D' and resid 1626 through 1644 removed outlier: 3.946A pdb=" N ARG D1636 " --> pdb=" O GLY D1632 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D1637 " --> pdb=" O LEU D1633 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL D1642 " --> pdb=" O ASP D1638 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D1644 " --> pdb=" O GLY D1640 " (cutoff:3.500A) Processing helix chain 'D' and resid 1647 through 1658 removed outlier: 3.686A pdb=" N THR D1658 " --> pdb=" O ALA D1654 " (cutoff:3.500A) Processing helix chain 'D' and resid 1673 through 1761 removed outlier: 3.849A pdb=" N HIS D1726 " --> pdb=" O GLU D1722 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN D1743 " --> pdb=" O GLN D1739 " (cutoff:3.500A) Processing helix chain 'D' and resid 1765 through 1802 removed outlier: 3.813A pdb=" N TRP D1771 " --> pdb=" O GLU D1767 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY D1778 " --> pdb=" O GLY D1774 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE D1781 " --> pdb=" O SER D1777 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D1782 " --> pdb=" O GLY D1778 " (cutoff:3.500A) Proline residue: D1789 - end of helix removed outlier: 4.031A pdb=" N LYS D1800 " --> pdb=" O ALA D1796 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU D1801 " --> pdb=" O VAL D1797 " (cutoff:3.500A) Processing helix chain 'D' and resid 1824 through 1843 removed outlier: 3.944A pdb=" N ASP D1828 " --> pdb=" O LEU D1824 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D1829 " --> pdb=" O ALA D1825 " (cutoff:3.500A) Processing helix chain 'D' and resid 1869 through 1878 Processing helix chain 'D' and resid 1907 through 1910 Processing helix chain 'E' and resid 59 through 68 Proline residue: E 64 - end of helix removed outlier: 3.537A pdb=" N THR E 68 " --> pdb=" O PRO E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 107 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.761A pdb=" N LEU E 128 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 137 Processing helix chain 'E' and resid 143 through 153 removed outlier: 3.845A pdb=" N LYS E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 161 removed outlier: 3.840A pdb=" N THR E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 172 removed outlier: 3.983A pdb=" N PHE E 171 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR E 172 " --> pdb=" O SER E 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 168 through 172' Processing helix chain 'E' and resid 176 through 189 removed outlier: 3.635A pdb=" N THR E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS E 189 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 199 removed outlier: 3.579A pdb=" N LEU E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 217 removed outlier: 3.726A pdb=" N GLN E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 245 Processing helix chain 'E' and resid 248 through 262 removed outlier: 3.725A pdb=" N LEU E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE E 260 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 288 removed outlier: 3.576A pdb=" N ILE E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 300 Processing helix chain 'E' and resid 313 through 319 Processing helix chain 'E' and resid 335 through 345 removed outlier: 4.362A pdb=" N ILE E 339 " --> pdb=" O SER E 335 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG E 341 " --> pdb=" O GLU E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 357 Processing helix chain 'E' and resid 372 through 387 removed outlier: 3.638A pdb=" N GLN E 376 " --> pdb=" O LYS E 372 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET E 380 " --> pdb=" O GLN E 376 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 381 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 383 " --> pdb=" O ARG E 379 " (cutoff:3.500A) Proline residue: E 384 - end of helix removed outlier: 3.578A pdb=" N LEU E 387 " --> pdb=" O ILE E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 401 removed outlier: 3.682A pdb=" N TYR E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 414 removed outlier: 3.698A pdb=" N LYS E 411 " --> pdb=" O ASN E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 437 removed outlier: 3.512A pdb=" N ILE E 420 " --> pdb=" O ASN E 416 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 424 " --> pdb=" O ILE E 420 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN E 437 " --> pdb=" O TRP E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 449 Processing helix chain 'E' and resid 457 through 470 removed outlier: 3.934A pdb=" N ASN E 466 " --> pdb=" O ASN E 462 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 467 " --> pdb=" O PHE E 463 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR E 468 " --> pdb=" O LEU E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 492 removed outlier: 4.020A pdb=" N ASN E 483 " --> pdb=" O SER E 479 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE E 492 " --> pdb=" O LEU E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 507 removed outlier: 3.715A pdb=" N ASN E 504 " --> pdb=" O ALA E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 525 removed outlier: 3.769A pdb=" N THR E 525 " --> pdb=" O ASN E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 538 Processing helix chain 'E' and resid 538 through 558 removed outlier: 4.003A pdb=" N LEU E 542 " --> pdb=" O HIS E 538 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN E 546 " --> pdb=" O LEU E 542 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR E 551 " --> pdb=" O LYS E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 569 removed outlier: 3.504A pdb=" N ILE E 565 " --> pdb=" O SER E 561 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 601 removed outlier: 3.984A pdb=" N SER E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 601 " --> pdb=" O CYS E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 617 removed outlier: 3.623A pdb=" N LEU E 608 " --> pdb=" O SER E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 661 removed outlier: 3.558A pdb=" N GLU E 624 " --> pdb=" O ASN E 620 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL E 633 " --> pdb=" O SER E 629 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN E 646 " --> pdb=" O GLY E 642 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER E 647 " --> pdb=" O SER E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 708 removed outlier: 4.052A pdb=" N LEU E 682 " --> pdb=" O GLU E 678 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS E 684 " --> pdb=" O SER E 680 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER E 685 " --> pdb=" O ASN E 681 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU E 695 " --> pdb=" O GLY E 691 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE E 698 " --> pdb=" O LYS E 694 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN E 708 " --> pdb=" O LYS E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 716 through 726 removed outlier: 3.626A pdb=" N ILE E 720 " --> pdb=" O SER E 716 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 742 removed outlier: 3.780A pdb=" N PHE E 737 " --> pdb=" O ALA E 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 799 removed outlier: 3.689A pdb=" N ASN E 791 " --> pdb=" O LEU E 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 802 through 815 removed outlier: 3.843A pdb=" N ILE E 806 " --> pdb=" O HIS E 802 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE E 807 " --> pdb=" O PRO E 803 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS E 808 " --> pdb=" O GLY E 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 828 removed outlier: 3.817A pdb=" N ASN E 826 " --> pdb=" O GLU E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 838 through 858 removed outlier: 3.595A pdb=" N ASP E 849 " --> pdb=" O GLU E 845 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA E 850 " --> pdb=" O SER E 846 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN E 853 " --> pdb=" O ASP E 849 " (cutoff:3.500A) Processing helix chain 'E' and resid 868 through 877 Processing helix chain 'E' and resid 889 through 907 removed outlier: 3.728A pdb=" N ASP E 907 " --> pdb=" O ASN E 903 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 922 removed outlier: 3.711A pdb=" N ILE E 918 " --> pdb=" O HIS E 914 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR E 920 " --> pdb=" O LYS E 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 948 Processing helix chain 'E' and resid 964 through 972 Processing helix chain 'E' and resid 980 through 999 removed outlier: 3.875A pdb=" N VAL E 984 " --> pdb=" O THR E 980 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 997 " --> pdb=" O ILE E 993 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 998 " --> pdb=" O SER E 994 " (cutoff:3.500A) Processing helix chain 'E' and resid 1268 through 1276 removed outlier: 3.685A pdb=" N GLN E1276 " --> pdb=" O VAL E1272 " (cutoff:3.500A) Processing helix chain 'E' and resid 1284 through 1290 removed outlier: 4.151A pdb=" N ASP E1290 " --> pdb=" O SER E1286 " (cutoff:3.500A) Processing helix chain 'E' and resid 1301 through 1323 removed outlier: 3.740A pdb=" N PHE E1305 " --> pdb=" O TYR E1301 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE E1312 " --> pdb=" O PHE E1308 " (cutoff:3.500A) Proline residue: E1313 - end of helix removed outlier: 3.619A pdb=" N ARG E1319 " --> pdb=" O LEU E1315 " (cutoff:3.500A) Processing helix chain 'E' and resid 1325 through 1334 removed outlier: 4.027A pdb=" N HIS E1331 " --> pdb=" O ASP E1327 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP E1332 " --> pdb=" O LEU E1328 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E1333 " --> pdb=" O ALA E1329 " (cutoff:3.500A) Processing helix chain 'E' and resid 1381 through 1389 removed outlier: 3.731A pdb=" N ILE E1385 " --> pdb=" O ASP E1381 " (cutoff:3.500A) Processing helix chain 'E' and resid 1390 through 1412 removed outlier: 3.530A pdb=" N PHE E1398 " --> pdb=" O LYS E1394 " (cutoff:3.500A) Processing helix chain 'E' and resid 1417 through 1436 removed outlier: 3.939A pdb=" N ILE E1426 " --> pdb=" O ALA E1422 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR E1427 " --> pdb=" O GLU E1423 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR E1428 " --> pdb=" O ALA E1424 " (cutoff:3.500A) Processing helix chain 'E' and resid 1470 through 1487 removed outlier: 3.911A pdb=" N TRP E1476 " --> pdb=" O LEU E1472 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP E1477 " --> pdb=" O LEU E1473 " (cutoff:3.500A) Processing helix chain 'E' and resid 1536 through 1624 removed outlier: 3.592A pdb=" N LEU E1540 " --> pdb=" O ARG E1536 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER E1546 " --> pdb=" O GLU E1542 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP E1566 " --> pdb=" O LEU E1562 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN E1583 " --> pdb=" O GLN E1579 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS E1586 " --> pdb=" O LEU E1582 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE E1593 " --> pdb=" O GLN E1589 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN E1594 " --> pdb=" O ASN E1590 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E1596 " --> pdb=" O ASN E1592 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU E1601 " --> pdb=" O GLN E1597 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER E1605 " --> pdb=" O GLU E1601 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E1606 " --> pdb=" O ALA E1602 " (cutoff:3.500A) Processing helix chain 'E' and resid 1626 through 1644 removed outlier: 3.946A pdb=" N ARG E1636 " --> pdb=" O GLY E1632 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE E1637 " --> pdb=" O LEU E1633 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL E1642 " --> pdb=" O ASP E1638 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E1644 " --> pdb=" O GLY E1640 " (cutoff:3.500A) Processing helix chain 'E' and resid 1647 through 1658 removed outlier: 3.687A pdb=" N THR E1658 " --> pdb=" O ALA E1654 " (cutoff:3.500A) Processing helix chain 'E' and resid 1673 through 1761 removed outlier: 3.849A pdb=" N HIS E1726 " --> pdb=" O GLU E1722 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN E1743 " --> pdb=" O GLN E1739 " (cutoff:3.500A) Processing helix chain 'E' and resid 1765 through 1802 removed outlier: 3.814A pdb=" N TRP E1771 " --> pdb=" O GLU E1767 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY E1778 " --> pdb=" O GLY E1774 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE E1781 " --> pdb=" O SER E1777 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN E1782 " --> pdb=" O GLY E1778 " (cutoff:3.500A) Proline residue: E1789 - end of helix removed outlier: 4.032A pdb=" N LYS E1800 " --> pdb=" O ALA E1796 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU E1801 " --> pdb=" O VAL E1797 " (cutoff:3.500A) Processing helix chain 'E' and resid 1824 through 1843 removed outlier: 3.944A pdb=" N ASP E1828 " --> pdb=" O LEU E1824 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E1829 " --> pdb=" O ALA E1825 " (cutoff:3.500A) Processing helix chain 'E' and resid 1869 through 1878 Processing helix chain 'E' and resid 1907 through 1910 Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.827A pdb=" N ALA A 326 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 367 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 748 through 749 Processing sheet with id=AA3, first strand: chain 'A' and resid 1002 through 1009 removed outlier: 6.423A pdb=" N LEU A1018 " --> pdb=" O ILE A1004 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU A1006 " --> pdb=" O PHE A1016 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE A1016 " --> pdb=" O GLU A1006 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR A1008 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A1014 " --> pdb=" O TYR A1008 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A1031 " --> pdb=" O PHE A1017 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1064 through 1069 removed outlier: 4.144A pdb=" N LEU A1073 " --> pdb=" O LYS A1101 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP A1077 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A1100 " --> pdb=" O ASN A1108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1064 through 1069 removed outlier: 4.144A pdb=" N LEU A1073 " --> pdb=" O LYS A1101 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP A1077 " --> pdb=" O ASN A1097 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1256 through 1257 removed outlier: 3.883A pdb=" N ILE A1261 " --> pdb=" O LEU A1257 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1662 through 1663 Processing sheet with id=AA8, first strand: chain 'A' and resid 1667 through 1668 Processing sheet with id=AA9, first strand: chain 'A' and resid 1848 through 1853 removed outlier: 6.791A pdb=" N HIS A2023 " --> pdb=" O ILE A1930 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE A1930 " --> pdb=" O HIS A2023 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG A2025 " --> pdb=" O LYS A1928 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1884 through 1885 removed outlier: 3.954A pdb=" N LYS A1885 " --> pdb=" O VAL A1893 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A1893 " --> pdb=" O LYS A1885 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1900 " --> pdb=" O PHE A2003 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1904 through 1905 Processing sheet with id=AB3, first strand: chain 'A' and resid 1946 through 1948 removed outlier: 3.825A pdb=" N ALA A1946 " --> pdb=" O ILE A1966 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.827A pdb=" N ALA B 326 " --> pdb=" O MET B 369 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 367 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 748 through 749 Processing sheet with id=AB6, first strand: chain 'B' and resid 1002 through 1009 removed outlier: 6.423A pdb=" N LEU B1018 " --> pdb=" O ILE B1004 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU B1006 " --> pdb=" O PHE B1016 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE B1016 " --> pdb=" O GLU B1006 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR B1008 " --> pdb=" O THR B1014 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B1014 " --> pdb=" O TYR B1008 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B1031 " --> pdb=" O PHE B1017 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1064 through 1069 removed outlier: 4.143A pdb=" N LEU B1073 " --> pdb=" O LYS B1101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP B1077 " --> pdb=" O ASN B1097 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B1100 " --> pdb=" O ASN B1108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1064 through 1069 removed outlier: 4.143A pdb=" N LEU B1073 " --> pdb=" O LYS B1101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP B1077 " --> pdb=" O ASN B1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1256 through 1257 removed outlier: 3.884A pdb=" N ILE B1261 " --> pdb=" O LEU B1257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1667 through 1668 Processing sheet with id=AC2, first strand: chain 'B' and resid 1848 through 1853 removed outlier: 6.790A pdb=" N HIS B2023 " --> pdb=" O ILE B1930 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE B1930 " --> pdb=" O HIS B2023 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG B2025 " --> pdb=" O LYS B1928 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1884 through 1885 removed outlier: 3.954A pdb=" N LYS B1885 " --> pdb=" O VAL B1893 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B1893 " --> pdb=" O LYS B1885 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B1900 " --> pdb=" O PHE B2003 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1904 through 1905 Processing sheet with id=AC5, first strand: chain 'B' and resid 1946 through 1948 removed outlier: 3.824A pdb=" N ALA B1946 " --> pdb=" O ILE B1966 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 326 through 328 removed outlier: 3.827A pdb=" N ALA C 326 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL C 367 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 748 through 749 Processing sheet with id=AC8, first strand: chain 'C' and resid 1002 through 1009 removed outlier: 6.423A pdb=" N LEU C1018 " --> pdb=" O ILE C1004 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU C1006 " --> pdb=" O PHE C1016 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE C1016 " --> pdb=" O GLU C1006 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR C1008 " --> pdb=" O THR C1014 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C1014 " --> pdb=" O TYR C1008 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C1031 " --> pdb=" O PHE C1017 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1064 through 1069 removed outlier: 4.143A pdb=" N LEU C1073 " --> pdb=" O LYS C1101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP C1077 " --> pdb=" O ASN C1097 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR C1100 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1064 through 1069 removed outlier: 4.143A pdb=" N LEU C1073 " --> pdb=" O LYS C1101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP C1077 " --> pdb=" O ASN C1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1256 through 1257 removed outlier: 3.883A pdb=" N ILE C1261 " --> pdb=" O LEU C1257 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1667 through 1668 Processing sheet with id=AD4, first strand: chain 'C' and resid 1848 through 1853 removed outlier: 6.790A pdb=" N HIS C2023 " --> pdb=" O ILE C1930 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE C1930 " --> pdb=" O HIS C2023 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG C2025 " --> pdb=" O LYS C1928 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1884 through 1885 removed outlier: 3.954A pdb=" N LYS C1885 " --> pdb=" O VAL C1893 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C1893 " --> pdb=" O LYS C1885 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C1900 " --> pdb=" O PHE C2003 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1904 through 1905 Processing sheet with id=AD7, first strand: chain 'C' and resid 1946 through 1948 removed outlier: 3.824A pdb=" N ALA C1946 " --> pdb=" O ILE C1966 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 326 through 328 removed outlier: 3.827A pdb=" N ALA D 326 " --> pdb=" O MET D 369 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL D 367 " --> pdb=" O PHE D 328 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 748 through 749 Processing sheet with id=AE1, first strand: chain 'D' and resid 1002 through 1009 removed outlier: 6.423A pdb=" N LEU D1018 " --> pdb=" O ILE D1004 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU D1006 " --> pdb=" O PHE D1016 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE D1016 " --> pdb=" O GLU D1006 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR D1008 " --> pdb=" O THR D1014 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D1014 " --> pdb=" O TYR D1008 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D1031 " --> pdb=" O PHE D1017 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1064 through 1069 removed outlier: 4.143A pdb=" N LEU D1073 " --> pdb=" O LYS D1101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP D1077 " --> pdb=" O ASN D1097 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D1100 " --> pdb=" O ASN D1108 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1064 through 1069 removed outlier: 4.143A pdb=" N LEU D1073 " --> pdb=" O LYS D1101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP D1077 " --> pdb=" O ASN D1097 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1256 through 1257 removed outlier: 3.884A pdb=" N ILE D1261 " --> pdb=" O LEU D1257 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1667 through 1668 Processing sheet with id=AE6, first strand: chain 'D' and resid 1848 through 1853 removed outlier: 6.791A pdb=" N HIS D2023 " --> pdb=" O ILE D1930 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE D1930 " --> pdb=" O HIS D2023 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG D2025 " --> pdb=" O LYS D1928 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1884 through 1885 removed outlier: 3.954A pdb=" N LYS D1885 " --> pdb=" O VAL D1893 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL D1893 " --> pdb=" O LYS D1885 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D1900 " --> pdb=" O PHE D2003 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1904 through 1905 Processing sheet with id=AE9, first strand: chain 'D' and resid 1946 through 1948 removed outlier: 3.824A pdb=" N ALA D1946 " --> pdb=" O ILE D1966 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 326 through 328 removed outlier: 3.826A pdb=" N ALA E 326 " --> pdb=" O MET E 369 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL E 367 " --> pdb=" O PHE E 328 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 748 through 749 Processing sheet with id=AF3, first strand: chain 'E' and resid 1002 through 1009 removed outlier: 6.423A pdb=" N LEU E1018 " --> pdb=" O ILE E1004 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU E1006 " --> pdb=" O PHE E1016 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE E1016 " --> pdb=" O GLU E1006 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR E1008 " --> pdb=" O THR E1014 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR E1014 " --> pdb=" O TYR E1008 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E1031 " --> pdb=" O PHE E1017 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 1064 through 1069 removed outlier: 4.142A pdb=" N LEU E1073 " --> pdb=" O LYS E1101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP E1077 " --> pdb=" O ASN E1097 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR E1100 " --> pdb=" O ASN E1108 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 1064 through 1069 removed outlier: 4.142A pdb=" N LEU E1073 " --> pdb=" O LYS E1101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP E1077 " --> pdb=" O ASN E1097 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 1256 through 1257 removed outlier: 3.883A pdb=" N ILE E1261 " --> pdb=" O LEU E1257 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 1848 through 1853 removed outlier: 6.790A pdb=" N HIS E2023 " --> pdb=" O ILE E1930 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE E1930 " --> pdb=" O HIS E2023 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG E2025 " --> pdb=" O LYS E1928 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 1884 through 1885 removed outlier: 3.954A pdb=" N LYS E1885 " --> pdb=" O VAL E1893 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL E1893 " --> pdb=" O LYS E1885 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E1900 " --> pdb=" O PHE E2003 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 1904 through 1905 Processing sheet with id=AG1, first strand: chain 'E' and resid 1946 through 1948 removed outlier: 3.824A pdb=" N ALA E1946 " --> pdb=" O ILE E1966 " (cutoff:3.500A) 3505 hydrogen bonds defined for protein. 10290 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: 32.89 Time building geometry restraints manager: 16.07 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: 20943 1.33 - 1.45: 13773 1.45 - 1.57: 41854 1.57 - 1.69: 0 1.69 - 1.81: 345 Bond restraints: 76915 Sorted by residual: bond pdb=" C ILE C 76 " pdb=" N PRO C 77 " ideal model delta sigma weight residual 1.329 1.375 -0.047 1.20e-02 6.94e+03 1.51e+01 bond pdb=" C ILE D 76 " pdb=" N PRO D 77 " ideal model delta sigma weight residual 1.329 1.375 -0.046 1.20e-02 6.94e+03 1.49e+01 bond pdb=" C ILE A 76 " pdb=" N PRO A 77 " ideal model delta sigma weight residual 1.329 1.375 -0.046 1.20e-02 6.94e+03 1.48e+01 bond pdb=" C ILE E 76 " pdb=" N PRO E 77 " ideal model delta sigma weight residual 1.329 1.375 -0.046 1.20e-02 6.94e+03 1.46e+01 bond pdb=" C ILE B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 1.329 1.374 -0.045 1.20e-02 6.94e+03 1.43e+01 ... (remaining 76910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 100721 2.39 - 4.78: 2823 4.78 - 7.17: 477 7.17 - 9.56: 124 9.56 - 11.95: 35 Bond angle restraints: 104180 Sorted by residual: angle pdb=" C ALA B1459 " pdb=" N GLU B1460 " pdb=" CA GLU B1460 " ideal model delta sigma weight residual 122.07 128.79 -6.72 1.43e+00 4.89e-01 2.21e+01 angle pdb=" C LYS E2011 " pdb=" N LEU E2012 " pdb=" CA LEU E2012 " ideal model delta sigma weight residual 121.54 130.41 -8.87 1.91e+00 2.74e-01 2.16e+01 angle pdb=" C LYS C2011 " pdb=" N LEU C2012 " pdb=" CA LEU C2012 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C LYS B2011 " pdb=" N LEU B2012 " pdb=" CA LEU B2012 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C LYS A2011 " pdb=" N LEU A2012 " pdb=" CA LEU A2012 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.13e+01 ... (remaining 104175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 43705 14.80 - 29.60: 2268 29.60 - 44.40: 557 44.40 - 59.20: 35 59.20 - 74.00: 50 Dihedral angle restraints: 46615 sinusoidal: 18975 harmonic: 27640 Sorted by residual: dihedral pdb=" CA SER B 231 " pdb=" C SER B 231 " pdb=" N PRO B 232 " pdb=" CA PRO B 232 " ideal model delta harmonic sigma weight residual 180.00 146.21 33.79 0 5.00e+00 4.00e-02 4.57e+01 dihedral pdb=" CA SER A 231 " pdb=" C SER A 231 " pdb=" N PRO A 232 " pdb=" CA PRO A 232 " ideal model delta harmonic sigma weight residual 180.00 146.23 33.77 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA SER E 231 " pdb=" C SER E 231 " pdb=" N PRO E 232 " pdb=" CA PRO E 232 " ideal model delta harmonic sigma weight residual 180.00 146.24 33.76 0 5.00e+00 4.00e-02 4.56e+01 ... (remaining 46612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 10475 0.092 - 0.184: 1005 0.184 - 0.276: 40 0.276 - 0.368: 0 0.368 - 0.459: 5 Chirality restraints: 11525 Sorted by residual: chirality pdb=" CB ILE C1129 " pdb=" CA ILE C1129 " pdb=" CG1 ILE C1129 " pdb=" CG2 ILE C1129 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CB ILE B1129 " pdb=" CA ILE B1129 " pdb=" CG1 ILE B1129 " pdb=" CG2 ILE B1129 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CB ILE A1129 " pdb=" CA ILE A1129 " pdb=" CG1 ILE A1129 " pdb=" CG2 ILE A1129 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.23e+00 ... (remaining 11522 not shown) Planarity restraints: 13555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 666 " -0.050 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO E 667 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 667 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 667 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 666 " 0.050 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO D 667 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 667 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 667 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 666 " -0.050 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO A 667 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 667 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 667 " -0.042 5.00e-02 4.00e+02 ... (remaining 13552 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 16422 2.78 - 3.31: 68944 3.31 - 3.84: 121859 3.84 - 4.37: 143878 4.37 - 4.90: 244437 Nonbonded interactions: 595540 Sorted by model distance: nonbonded pdb=" OH TYR D 452 " pdb=" OE1 GLN D 550 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR B 452 " pdb=" OE1 GLN B 550 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR E 452 " pdb=" OE1 GLN E 550 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 452 " pdb=" OE1 GLN A 550 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR C 452 " pdb=" OE1 GLN C 550 " model vdw 2.254 3.040 ... (remaining 595535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 11.300 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: 0.060 Extract box with map and model: 2.670 Check model and map are aligned: 0.440 Set scattering table: 0.570 Process input model: 146.640 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.250 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: 0.030 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 76915 Z= 0.374 Angle : 0.993 11.954 104180 Z= 0.520 Chirality : 0.054 0.459 11525 Planarity : 0.007 0.074 13555 Dihedral : 10.244 74.002 28715 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 0.36 % Allowed : 1.87 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.07), residues: 9345 helix: -2.22 (0.06), residues: 4910 sheet: -2.75 (0.20), residues: 490 loop : -3.27 (0.08), residues: 3945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 505 HIS 0.021 0.002 HIS B1751 PHE 0.035 0.003 PHE A1320 TYR 0.043 0.003 TYR D1677 ARG 0.008 0.001 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2160 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 2130 time to evaluate : 6.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 TYR cc_start: 0.6513 (t80) cc_final: 0.6310 (t80) REVERT: A 418 LEU cc_start: 0.7942 (mt) cc_final: 0.7727 (mm) REVERT: A 432 GLN cc_start: 0.8365 (tp40) cc_final: 0.8131 (pt0) REVERT: A 533 HIS cc_start: 0.7368 (m-70) cc_final: 0.7118 (m-70) REVERT: A 801 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8471 (tt) REVERT: A 849 ASP cc_start: 0.8031 (m-30) cc_final: 0.7786 (m-30) REVERT: A 1399 MET cc_start: 0.7628 (mtm) cc_final: 0.7164 (mtt) REVERT: A 1403 ASP cc_start: 0.7040 (m-30) cc_final: 0.6708 (m-30) REVERT: A 1468 TYR cc_start: 0.6483 (t80) cc_final: 0.5877 (t80) REVERT: A 1566 ASP cc_start: 0.7945 (m-30) cc_final: 0.7729 (m-30) REVERT: A 1629 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 1748 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7066 (mt-10) REVERT: B 401 TYR cc_start: 0.6500 (t80) cc_final: 0.6247 (t80) REVERT: B 412 ILE cc_start: 0.8109 (mt) cc_final: 0.7895 (mp) REVERT: B 432 GLN cc_start: 0.8321 (tp40) cc_final: 0.8088 (pt0) REVERT: B 698 ILE cc_start: 0.7798 (mt) cc_final: 0.7449 (tp) REVERT: B 801 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8469 (tt) REVERT: B 849 ASP cc_start: 0.8067 (m-30) cc_final: 0.7793 (m-30) REVERT: B 934 TYR cc_start: 0.7346 (m-80) cc_final: 0.6917 (m-10) REVERT: B 1110 ASN cc_start: 0.8628 (m-40) cc_final: 0.8226 (m-40) REVERT: B 1399 MET cc_start: 0.7569 (mtm) cc_final: 0.6979 (mtt) REVERT: B 1403 ASP cc_start: 0.7070 (m-30) cc_final: 0.6737 (m-30) REVERT: B 1468 TYR cc_start: 0.6448 (t80) cc_final: 0.5879 (t80) REVERT: B 1519 ASN cc_start: 0.6804 (m110) cc_final: 0.6383 (m-40) REVERT: B 1566 ASP cc_start: 0.8029 (m-30) cc_final: 0.7702 (m-30) REVERT: B 1629 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8084 (mt-10) REVERT: C 324 VAL cc_start: 0.6976 (t) cc_final: 0.6435 (t) REVERT: C 401 TYR cc_start: 0.6558 (t80) cc_final: 0.6293 (t80) REVERT: C 412 ILE cc_start: 0.8153 (mt) cc_final: 0.7924 (mp) REVERT: C 418 LEU cc_start: 0.7850 (mt) cc_final: 0.7425 (mm) REVERT: C 432 GLN cc_start: 0.8426 (tp40) cc_final: 0.8115 (pt0) REVERT: C 533 HIS cc_start: 0.7285 (m-70) cc_final: 0.7021 (m-70) REVERT: C 801 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8488 (tt) REVERT: C 849 ASP cc_start: 0.8007 (m-30) cc_final: 0.7694 (m-30) REVERT: C 934 TYR cc_start: 0.7339 (m-80) cc_final: 0.6877 (m-10) REVERT: C 1110 ASN cc_start: 0.8664 (m-40) cc_final: 0.8362 (m-40) REVERT: C 1399 MET cc_start: 0.7667 (mtm) cc_final: 0.7198 (mtt) REVERT: C 1403 ASP cc_start: 0.7009 (m-30) cc_final: 0.6690 (m-30) REVERT: C 1468 TYR cc_start: 0.6451 (t80) cc_final: 0.5898 (t80) REVERT: C 1519 ASN cc_start: 0.6712 (m110) cc_final: 0.5898 (m110) REVERT: C 1566 ASP cc_start: 0.8015 (m-30) cc_final: 0.7722 (m-30) REVERT: C 1629 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7982 (mt-10) REVERT: D 401 TYR cc_start: 0.6495 (t80) cc_final: 0.6263 (t80) REVERT: D 432 GLN cc_start: 0.8429 (tp40) cc_final: 0.7914 (pt0) REVERT: D 533 HIS cc_start: 0.7297 (m-70) cc_final: 0.7056 (m170) REVERT: D 542 LEU cc_start: 0.8917 (mt) cc_final: 0.8620 (mt) REVERT: D 677 LEU cc_start: 0.8147 (mm) cc_final: 0.7512 (pp) REVERT: D 801 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8471 (tt) REVERT: D 849 ASP cc_start: 0.7964 (m-30) cc_final: 0.7701 (m-30) REVERT: D 934 TYR cc_start: 0.7279 (m-80) cc_final: 0.6934 (m-10) REVERT: D 1072 ARG cc_start: 0.7370 (mtt180) cc_final: 0.7131 (mtt-85) REVERT: D 1110 ASN cc_start: 0.8706 (m-40) cc_final: 0.8315 (m-40) REVERT: D 1381 ASP cc_start: 0.7726 (t0) cc_final: 0.7503 (t70) REVERT: D 1399 MET cc_start: 0.7651 (mtm) cc_final: 0.7032 (mtt) REVERT: D 1403 ASP cc_start: 0.7021 (m-30) cc_final: 0.6705 (m-30) REVERT: D 1468 TYR cc_start: 0.6529 (t80) cc_final: 0.6004 (t80) REVERT: D 1519 ASN cc_start: 0.6686 (m110) cc_final: 0.6003 (m110) REVERT: D 1566 ASP cc_start: 0.7982 (m-30) cc_final: 0.7773 (m-30) REVERT: D 1629 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8011 (mt-10) REVERT: E 177 ASP cc_start: 0.7460 (t0) cc_final: 0.7164 (t70) REVERT: E 401 TYR cc_start: 0.6451 (t80) cc_final: 0.6216 (t80) REVERT: E 418 LEU cc_start: 0.7861 (mt) cc_final: 0.7492 (mm) REVERT: E 432 GLN cc_start: 0.8310 (tp40) cc_final: 0.8014 (pt0) REVERT: E 801 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8441 (tt) REVERT: E 849 ASP cc_start: 0.8066 (m-30) cc_final: 0.7547 (m-30) REVERT: E 934 TYR cc_start: 0.7301 (m-80) cc_final: 0.6814 (m-10) REVERT: E 1110 ASN cc_start: 0.8632 (m-40) cc_final: 0.8099 (m-40) REVERT: E 1399 MET cc_start: 0.7666 (mtm) cc_final: 0.7065 (mtt) REVERT: E 1403 ASP cc_start: 0.7028 (m-30) cc_final: 0.6698 (m-30) REVERT: E 1468 TYR cc_start: 0.6656 (t80) cc_final: 0.5716 (t80) REVERT: E 1519 ASN cc_start: 0.6801 (m110) cc_final: 0.6307 (m-40) REVERT: E 1566 ASP cc_start: 0.7926 (m-30) cc_final: 0.7723 (m-30) REVERT: E 1629 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8065 (mt-10) REVERT: E 1756 TYR cc_start: 0.8702 (t80) cc_final: 0.8345 (t80) outliers start: 30 outliers final: 5 residues processed: 2145 average time/residue: 0.7937 time to fit residues: 2852.5127 Evaluate side-chains 958 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 948 time to evaluate : 6.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 1314 PHE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 1314 PHE Chi-restraints excluded: chain E residue 801 ILE Chi-restraints excluded: chain E residue 1314 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 789 optimal weight: 6.9990 chunk 708 optimal weight: 0.8980 chunk 393 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 478 optimal weight: 0.9990 chunk 378 optimal weight: 5.9990 chunk 732 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 445 optimal weight: 0.8980 chunk 545 optimal weight: 0.0980 chunk 849 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS A 117 HIS A 256 ASN A 258 ASN A 437 GLN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN A 490 ASN A 509 ASN A 556 GLN A 598 GLN A 605 GLN A 623 GLN A 702 GLN ** A 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN ** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS A 823 ASN A 831 ASN A 914 HIS A 921 HIS A 976 ASN A 989 GLN A1071 ASN A1311 HIS A1408 GLN A1469 ASN ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1519 ASN A1575 GLN A1684 GLN A1739 GLN ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1788 GLN A1858 GLN A1884 GLN ** A1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1954 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS B 117 HIS B 256 ASN B 258 ASN B 437 GLN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN B 490 ASN B 509 ASN ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN B 702 GLN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 ASN ** B 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 ASN B 792 HIS B 823 ASN B 831 ASN B 914 HIS B 921 HIS B1071 ASN B1110 ASN B1311 HIS B1330 GLN B1463 HIS B1469 ASN ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1519 ASN B1575 GLN B1684 GLN B1788 GLN B1834 GLN B1838 ASN B1845 GLN B1858 GLN B1884 GLN ** B1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1954 ASN C 104 HIS C 117 HIS C 256 ASN C 258 ASN C 329 ASN ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN C 445 GLN C 466 ASN C 490 ASN C 509 ASN C 556 GLN C 598 GLN C 623 GLN C 702 GLN ** C 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 ASN ** C 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 HIS C 823 ASN C 831 ASN C 914 HIS C 921 HIS C 976 ASN C1071 ASN C1110 ASN C1311 HIS C1463 HIS C1469 ASN ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1519 ASN C1575 GLN C1591 ASN C1684 GLN ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1788 GLN C1845 GLN C1858 GLN C1884 GLN ** C1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1954 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS D 117 HIS D 256 ASN D 258 ASN D 310 ASN D 437 GLN ** D 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 ASN D 490 ASN D 509 ASN D 539 GLN ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN D 702 GLN ** D 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 ASN D 792 HIS D 823 ASN D 831 ASN D 914 HIS D 921 HIS D 976 ASN D1071 ASN D1110 ASN D1311 HIS D1330 GLN D1408 GLN D1463 HIS D1469 ASN ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1519 ASN D1575 GLN D1591 ASN D1592 ASN D1684 GLN D1788 GLN D1834 GLN D1845 GLN D1858 GLN D1884 GLN ** D1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1954 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS E 117 HIS E 256 ASN E 258 ASN E 329 ASN E 437 GLN ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN E 509 ASN E 556 GLN E 598 GLN E 623 GLN E 702 GLN ** E 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 713 ASN ** E 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 791 ASN E 792 HIS E 823 ASN E 831 ASN E 914 HIS E 921 HIS E 976 ASN E1071 ASN E1110 ASN E1311 HIS E1330 GLN E1463 HIS E1469 ASN E1519 ASN E1575 GLN E1591 ASN E1684 GLN E1788 GLN E1834 GLN E1845 GLN E1858 GLN E1884 GLN ** E1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1954 ASN Total number of N/Q/H flips: 174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 76915 Z= 0.183 Angle : 0.636 12.697 104180 Z= 0.328 Chirality : 0.041 0.219 11525 Planarity : 0.005 0.073 13555 Dihedral : 6.093 58.765 10115 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.02 % Allowed : 9.20 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.08), residues: 9345 helix: -0.34 (0.07), residues: 5040 sheet: -2.08 (0.22), residues: 435 loop : -2.95 (0.09), residues: 3870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1068 HIS 0.006 0.001 HIS C1751 PHE 0.020 0.002 PHE B1308 TYR 0.017 0.002 TYR C 950 ARG 0.006 0.001 ARG E1072 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1049 time to evaluate : 6.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 TYR cc_start: 0.6423 (t80) cc_final: 0.6108 (t80) REVERT: A 422 ASP cc_start: 0.7292 (m-30) cc_final: 0.7071 (m-30) REVERT: A 457 THR cc_start: 0.8206 (p) cc_final: 0.7787 (p) REVERT: A 671 MET cc_start: 0.5630 (mtp) cc_final: 0.5114 (mmm) REVERT: A 1318 MET cc_start: 0.8208 (mmp) cc_final: 0.8002 (mmp) REVERT: A 1399 MET cc_start: 0.7725 (mtm) cc_final: 0.7236 (mtt) REVERT: A 1403 ASP cc_start: 0.7104 (m-30) cc_final: 0.6769 (m-30) REVERT: A 1468 TYR cc_start: 0.6645 (t80) cc_final: 0.5916 (t80) REVERT: A 1626 SER cc_start: 0.8785 (t) cc_final: 0.8585 (p) REVERT: A 2012 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8431 (tp) REVERT: B 401 TYR cc_start: 0.6530 (t80) cc_final: 0.6177 (t80) REVERT: B 414 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: B 432 GLN cc_start: 0.8326 (tp40) cc_final: 0.8118 (pt0) REVERT: B 440 ASP cc_start: 0.6962 (p0) cc_final: 0.6664 (p0) REVERT: B 457 THR cc_start: 0.8119 (p) cc_final: 0.7124 (p) REVERT: B 671 MET cc_start: 0.6546 (mtt) cc_final: 0.6082 (mmm) REVERT: B 696 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7349 (mp0) REVERT: B 934 TYR cc_start: 0.7171 (m-80) cc_final: 0.6814 (m-10) REVERT: B 1399 MET cc_start: 0.7680 (mtm) cc_final: 0.7021 (mtt) REVERT: B 1403 ASP cc_start: 0.7112 (m-30) cc_final: 0.6776 (m-30) REVERT: B 1468 TYR cc_start: 0.6660 (t80) cc_final: 0.5932 (t80) REVERT: B 1704 ASP cc_start: 0.7382 (m-30) cc_final: 0.7069 (m-30) REVERT: B 1767 GLU cc_start: 0.7544 (tt0) cc_final: 0.7344 (tt0) REVERT: B 2012 LEU cc_start: 0.8630 (pp) cc_final: 0.8311 (tp) REVERT: C 411 LYS cc_start: 0.8628 (mttt) cc_final: 0.8384 (ptmm) REVERT: C 422 ASP cc_start: 0.7123 (m-30) cc_final: 0.6895 (m-30) REVERT: C 432 GLN cc_start: 0.8387 (tp40) cc_final: 0.8077 (pt0) REVERT: C 457 THR cc_start: 0.8122 (p) cc_final: 0.7226 (p) REVERT: C 533 HIS cc_start: 0.7378 (m-70) cc_final: 0.7177 (m90) REVERT: C 648 MET cc_start: 0.7986 (tmm) cc_final: 0.7459 (tmm) REVERT: C 671 MET cc_start: 0.6718 (mtt) cc_final: 0.6224 (mmm) REVERT: C 849 ASP cc_start: 0.8189 (m-30) cc_final: 0.7969 (m-30) REVERT: C 934 TYR cc_start: 0.7150 (m-80) cc_final: 0.6775 (m-10) REVERT: C 1468 TYR cc_start: 0.6510 (t80) cc_final: 0.5665 (t80) REVERT: C 1626 SER cc_start: 0.8776 (t) cc_final: 0.8202 (p) REVERT: C 1767 GLU cc_start: 0.7578 (tt0) cc_final: 0.7341 (tt0) REVERT: C 1793 MET cc_start: 0.7942 (mtm) cc_final: 0.7739 (mtm) REVERT: C 2012 LEU cc_start: 0.8574 (pp) cc_final: 0.8274 (tp) REVERT: D 300 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7546 (m-40) REVERT: D 414 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7677 (mp10) REVERT: D 432 GLN cc_start: 0.8329 (tp40) cc_final: 0.8123 (pt0) REVERT: D 457 THR cc_start: 0.8110 (p) cc_final: 0.7123 (p) REVERT: D 533 HIS cc_start: 0.7417 (m-70) cc_final: 0.7133 (m170) REVERT: D 671 MET cc_start: 0.6694 (mtt) cc_final: 0.6242 (mmm) REVERT: D 696 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7446 (mp0) REVERT: D 934 TYR cc_start: 0.7125 (m-80) cc_final: 0.6905 (m-10) REVERT: D 1399 MET cc_start: 0.7747 (mtm) cc_final: 0.6975 (mtt) REVERT: D 1403 ASP cc_start: 0.7125 (m-30) cc_final: 0.6753 (m-30) REVERT: D 1468 TYR cc_start: 0.6611 (t80) cc_final: 0.6011 (t80) REVERT: D 1767 GLU cc_start: 0.7510 (tt0) cc_final: 0.7298 (tt0) REVERT: D 2012 LEU cc_start: 0.8768 (pp) cc_final: 0.8477 (tp) REVERT: E 414 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: E 457 THR cc_start: 0.8161 (p) cc_final: 0.7627 (p) REVERT: E 556 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8360 (mt0) REVERT: E 648 MET cc_start: 0.7764 (tmm) cc_final: 0.7325 (tmm) REVERT: E 671 MET cc_start: 0.6726 (mtt) cc_final: 0.6270 (mmm) REVERT: E 822 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8003 (pm20) REVERT: E 1110 ASN cc_start: 0.8391 (m110) cc_final: 0.8111 (m-40) REVERT: E 1318 MET cc_start: 0.8152 (mmp) cc_final: 0.7948 (mmp) REVERT: E 1704 ASP cc_start: 0.7386 (m-30) cc_final: 0.7068 (m-30) REVERT: E 1756 TYR cc_start: 0.8748 (t80) cc_final: 0.8308 (t80) REVERT: E 2012 LEU cc_start: 0.8632 (pp) cc_final: 0.8305 (tp) outliers start: 167 outliers final: 82 residues processed: 1178 average time/residue: 0.7002 time to fit residues: 1423.0367 Evaluate side-chains 807 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 719 time to evaluate : 6.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1519 ASN Chi-restraints excluded: chain A residue 1575 GLN Chi-restraints excluded: chain A residue 1615 LYS Chi-restraints excluded: chain A residue 1707 GLU Chi-restraints excluded: chain A residue 1739 GLN Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1575 GLN Chi-restraints excluded: chain B residue 1768 LEU Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 772 MET Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 1314 PHE Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1575 GLN Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1314 PHE Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1420 THR Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1575 GLN Chi-restraints excluded: chain D residue 1579 GLN Chi-restraints excluded: chain D residue 1627 SER Chi-restraints excluded: chain D residue 1707 GLU Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1808 ASP Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 556 GLN Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 1027 GLN Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1314 PHE Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1575 GLN Chi-restraints excluded: chain E residue 1615 LYS Chi-restraints excluded: chain E residue 1707 GLU Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1808 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 471 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 706 optimal weight: 0.8980 chunk 578 optimal weight: 0.7980 chunk 234 optimal weight: 0.4980 chunk 850 optimal weight: 5.9990 chunk 918 optimal weight: 3.9990 chunk 757 optimal weight: 7.9990 chunk 843 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 682 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN A 533 HIS A 598 GLN ** A 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN ** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1519 ASN A1591 ASN A1684 GLN A1716 GLN ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 393 GLN B 466 ASN B 490 ASN ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 ASN ** B 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1591 ASN B1716 GLN B1739 GLN ** B1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN C 556 GLN ** C 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN ** C 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1716 GLN ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN D 466 ASN ** D 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 753 ASN D1348 ASN D1408 GLN D1716 GLN ** D1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN E 286 GLN E 466 ASN E 490 ASN ** E 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 753 ASN ** E 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1716 GLN ** E1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 76915 Z= 0.197 Angle : 0.605 11.680 104180 Z= 0.309 Chirality : 0.040 0.228 11525 Planarity : 0.004 0.069 13555 Dihedral : 5.529 47.694 10105 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.19 % Allowed : 11.23 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.09), residues: 9345 helix: 0.42 (0.08), residues: 5075 sheet: -1.55 (0.23), residues: 435 loop : -2.76 (0.09), residues: 3835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1672 HIS 0.010 0.001 HIS D1042 PHE 0.017 0.002 PHE B1976 TYR 0.013 0.001 TYR D1780 ARG 0.008 0.000 ARG D1628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 801 time to evaluate : 6.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.7534 (OUTLIER) cc_final: 0.7232 (t) REVERT: A 401 TYR cc_start: 0.6379 (t80) cc_final: 0.6008 (t80) REVERT: A 414 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7703 (mp10) REVERT: A 497 ASN cc_start: 0.8480 (m110) cc_final: 0.8257 (m-40) REVERT: A 671 MET cc_start: 0.5640 (mtp) cc_final: 0.5178 (mmm) REVERT: A 713 ASN cc_start: 0.6200 (OUTLIER) cc_final: 0.5878 (p0) REVERT: A 1399 MET cc_start: 0.7706 (mtm) cc_final: 0.7239 (mtt) REVERT: A 1403 ASP cc_start: 0.7152 (m-30) cc_final: 0.6781 (m-30) REVERT: A 1593 ILE cc_start: 0.8854 (pt) cc_final: 0.8581 (mt) REVERT: A 2012 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8409 (tp) REVERT: B 231 SER cc_start: 0.7665 (OUTLIER) cc_final: 0.7249 (t) REVERT: B 300 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7715 (m-40) REVERT: B 432 GLN cc_start: 0.8365 (tp40) cc_final: 0.8093 (pt0) REVERT: B 671 MET cc_start: 0.6615 (mtt) cc_final: 0.6173 (mmm) REVERT: B 677 LEU cc_start: 0.8239 (mt) cc_final: 0.7939 (mp) REVERT: B 934 TYR cc_start: 0.7157 (m-80) cc_final: 0.6887 (m-10) REVERT: B 1072 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7653 (mpp80) REVERT: B 2012 LEU cc_start: 0.8545 (pp) cc_final: 0.8249 (tp) REVERT: C 231 SER cc_start: 0.7719 (OUTLIER) cc_final: 0.7330 (t) REVERT: C 361 LYS cc_start: 0.6067 (tppt) cc_final: 0.5699 (tppp) REVERT: C 411 LYS cc_start: 0.8615 (mttt) cc_final: 0.8382 (ptmm) REVERT: C 432 GLN cc_start: 0.8368 (tp40) cc_final: 0.8088 (pt0) REVERT: C 533 HIS cc_start: 0.7498 (m-70) cc_final: 0.7130 (m-70) REVERT: C 648 MET cc_start: 0.7985 (tmm) cc_final: 0.7454 (tmm) REVERT: C 849 ASP cc_start: 0.8282 (m-30) cc_final: 0.8021 (m-30) REVERT: C 954 TYR cc_start: 0.8041 (m-10) cc_final: 0.7763 (m-80) REVERT: C 1532 THR cc_start: 0.7035 (t) cc_final: 0.6813 (m) REVERT: C 2012 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8269 (tp) REVERT: D 231 SER cc_start: 0.7678 (OUTLIER) cc_final: 0.7280 (t) REVERT: D 300 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7656 (m110) REVERT: D 414 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7739 (mp10) REVERT: D 432 GLN cc_start: 0.8356 (tp40) cc_final: 0.8088 (pt0) REVERT: D 671 MET cc_start: 0.6731 (mtt) cc_final: 0.6227 (mmm) REVERT: D 696 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7253 (mp0) REVERT: D 1399 MET cc_start: 0.7764 (mtm) cc_final: 0.7210 (mtt) REVERT: D 1403 ASP cc_start: 0.7133 (m-30) cc_final: 0.6807 (m-30) REVERT: D 1756 TYR cc_start: 0.8870 (t80) cc_final: 0.8550 (t80) REVERT: D 1793 MET cc_start: 0.8071 (mtm) cc_final: 0.7744 (mtm) REVERT: D 2012 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8489 (tp) REVERT: E 231 SER cc_start: 0.7684 (OUTLIER) cc_final: 0.7243 (t) REVERT: E 300 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7519 (m-40) REVERT: E 414 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: E 648 MET cc_start: 0.7771 (tmm) cc_final: 0.7380 (tmm) REVERT: E 671 MET cc_start: 0.6666 (mtt) cc_final: 0.6174 (mmm) REVERT: E 822 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7974 (pm20) REVERT: E 1110 ASN cc_start: 0.8363 (m110) cc_final: 0.8043 (m-40) REVERT: E 1269 LEU cc_start: 0.8141 (tp) cc_final: 0.7814 (mp) REVERT: E 1756 TYR cc_start: 0.8755 (t80) cc_final: 0.8295 (t80) REVERT: E 1878 MET cc_start: 0.5974 (mmp) cc_final: 0.5676 (mmm) REVERT: E 2012 LEU cc_start: 0.8605 (pp) cc_final: 0.8264 (tp) outliers start: 181 outliers final: 112 residues processed: 937 average time/residue: 0.6858 time to fit residues: 1122.8855 Evaluate side-chains 797 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 669 time to evaluate : 6.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 GLN Chi-restraints excluded: chain A residue 1615 LYS Chi-restraints excluded: chain A residue 1627 SER Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1707 GLU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1416 LEU Chi-restraints excluded: chain B residue 1642 VAL Chi-restraints excluded: chain B residue 1644 ILE Chi-restraints excluded: chain B residue 1768 LEU Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1269 LEU Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1627 SER Chi-restraints excluded: chain C residue 1642 VAL Chi-restraints excluded: chain C residue 1644 ILE Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 977 SER Chi-restraints excluded: chain D residue 1055 ILE Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1294 LEU Chi-restraints excluded: chain D residue 1314 PHE Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1642 VAL Chi-restraints excluded: chain D residue 1644 ILE Chi-restraints excluded: chain D residue 1707 GLU Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1808 ASP Chi-restraints excluded: chain D residue 2012 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 597 CYS Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 886 VAL Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 1027 GLN Chi-restraints excluded: chain E residue 1055 ILE Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1314 PHE Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1615 LYS Chi-restraints excluded: chain E residue 1644 ILE Chi-restraints excluded: chain E residue 1707 GLU Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1808 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 840 optimal weight: 1.9990 chunk 639 optimal weight: 6.9990 chunk 441 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 405 optimal weight: 7.9990 chunk 571 optimal weight: 1.9990 chunk 853 optimal weight: 2.9990 chunk 903 optimal weight: 4.9990 chunk 446 optimal weight: 9.9990 chunk 809 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN ** A1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 ASN A1330 GLN ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1838 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN C 329 ASN ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1408 GLN ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 844 ASN D 976 ASN D1079 ASN ** D1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1788 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 GLN ** E1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1079 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 76915 Z= 0.243 Angle : 0.607 11.644 104180 Z= 0.310 Chirality : 0.042 0.252 11525 Planarity : 0.004 0.051 13555 Dihedral : 5.271 30.498 10099 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.57 % Allowed : 12.12 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.09), residues: 9345 helix: 0.86 (0.08), residues: 5065 sheet: -1.44 (0.23), residues: 475 loop : -2.68 (0.09), residues: 3805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 505 HIS 0.008 0.001 HIS B1751 PHE 0.016 0.002 PHE B1976 TYR 0.016 0.002 TYR A1820 ARG 0.008 0.001 ARG D1628 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 744 time to evaluate : 6.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7253 (t) REVERT: A 588 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8962 (mp) REVERT: A 671 MET cc_start: 0.5732 (mtp) cc_final: 0.5272 (mmm) REVERT: A 2012 LEU cc_start: 0.8693 (pp) cc_final: 0.8393 (tp) REVERT: B 231 SER cc_start: 0.7789 (OUTLIER) cc_final: 0.7335 (t) REVERT: B 300 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7685 (m-40) REVERT: B 414 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: B 432 GLN cc_start: 0.8381 (tp40) cc_final: 0.8088 (pt0) REVERT: B 677 LEU cc_start: 0.8148 (mt) cc_final: 0.7874 (mp) REVERT: B 934 TYR cc_start: 0.7141 (m-80) cc_final: 0.6510 (m-10) REVERT: B 954 TYR cc_start: 0.8017 (m-10) cc_final: 0.7657 (m-80) REVERT: B 1072 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7638 (mpp80) REVERT: B 1471 ILE cc_start: 0.8412 (mm) cc_final: 0.8181 (mp) REVERT: B 1878 MET cc_start: 0.5979 (mmp) cc_final: 0.5609 (mmm) REVERT: B 2012 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8198 (tp) REVERT: C 231 SER cc_start: 0.7833 (OUTLIER) cc_final: 0.7371 (t) REVERT: C 432 GLN cc_start: 0.8436 (tp40) cc_final: 0.8090 (pt0) REVERT: C 648 MET cc_start: 0.7980 (tmm) cc_final: 0.7583 (tmm) REVERT: C 845 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7075 (tm-30) REVERT: C 849 ASP cc_start: 0.8330 (m-30) cc_final: 0.7977 (m-30) REVERT: C 954 TYR cc_start: 0.8147 (m-10) cc_final: 0.7909 (m-80) REVERT: C 1532 THR cc_start: 0.7108 (t) cc_final: 0.6899 (m) REVERT: C 1878 MET cc_start: 0.5810 (mmp) cc_final: 0.5527 (mmm) REVERT: C 2012 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8284 (tp) REVERT: D 231 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7395 (t) REVERT: D 300 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7593 (m110) REVERT: D 354 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8638 (tt) REVERT: D 414 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: D 432 GLN cc_start: 0.8396 (tp40) cc_final: 0.8080 (pt0) REVERT: D 588 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9033 (mp) REVERT: D 696 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7261 (mp0) REVERT: D 918 ILE cc_start: 0.7990 (mt) cc_final: 0.7696 (tp) REVERT: D 1399 MET cc_start: 0.7770 (mtm) cc_final: 0.7261 (mtt) REVERT: D 1403 ASP cc_start: 0.7149 (m-30) cc_final: 0.6858 (m-30) REVERT: D 1527 MET cc_start: 0.7052 (mtm) cc_final: 0.6847 (mtm) REVERT: D 2012 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8504 (tp) REVERT: E 231 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.7327 (t) REVERT: E 300 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7684 (m110) REVERT: E 822 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7968 (pm20) REVERT: E 1110 ASN cc_start: 0.8370 (m110) cc_final: 0.8025 (m-40) REVERT: E 1318 MET cc_start: 0.8040 (mmp) cc_final: 0.7829 (mmp) REVERT: E 1756 TYR cc_start: 0.8813 (t80) cc_final: 0.8294 (t80) REVERT: E 2012 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8229 (tp) outliers start: 213 outliers final: 126 residues processed: 903 average time/residue: 0.6879 time to fit residues: 1079.6452 Evaluate side-chains 808 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 664 time to evaluate : 6.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 GLN Chi-restraints excluded: chain A residue 1481 ILE Chi-restraints excluded: chain A residue 1579 GLN Chi-restraints excluded: chain A residue 1615 LYS Chi-restraints excluded: chain A residue 1627 SER Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 772 MET Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1076 ASP Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1416 LEU Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1642 VAL Chi-restraints excluded: chain B residue 1644 ILE Chi-restraints excluded: chain B residue 1739 GLN Chi-restraints excluded: chain B residue 1768 LEU Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1269 LEU Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1642 VAL Chi-restraints excluded: chain C residue 1644 ILE Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 977 SER Chi-restraints excluded: chain D residue 1055 ILE Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1076 ASP Chi-restraints excluded: chain D residue 1294 LEU Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1534 LEU Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1579 GLN Chi-restraints excluded: chain D residue 1642 VAL Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1808 ASP Chi-restraints excluded: chain D residue 2012 LEU Chi-restraints excluded: chain D residue 2027 THR Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 597 CYS Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 886 VAL Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 1027 GLN Chi-restraints excluded: chain E residue 1055 ILE Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1076 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1445 HIS Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1615 LYS Chi-restraints excluded: chain E residue 1627 SER Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1644 ILE Chi-restraints excluded: chain E residue 1707 GLU Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1808 ASP Chi-restraints excluded: chain E residue 2012 LEU Chi-restraints excluded: chain E residue 2027 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 752 optimal weight: 0.6980 chunk 513 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 672 optimal weight: 2.9990 chunk 372 optimal weight: 10.0000 chunk 771 optimal weight: 0.8980 chunk 624 optimal weight: 6.9990 chunk 1 optimal weight: 0.0370 chunk 461 optimal weight: 0.5980 chunk 811 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 563 GLN A 605 GLN ** A1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1388 GLN A1463 HIS ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1788 GLN A1929 GLN B 90 GLN B 329 ASN ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1388 GLN ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1515 HIS B1929 GLN C 90 GLN C 286 GLN C 333 GLN C1079 ASN C1388 GLN ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1788 GLN ** C1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1929 GLN D 90 GLN D 844 ASN D1388 GLN ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1929 GLN D1977 GLN E 90 GLN E 286 GLN E1388 GLN E1929 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 76915 Z= 0.151 Angle : 0.554 11.623 104180 Z= 0.282 Chirality : 0.039 0.251 11525 Planarity : 0.004 0.051 13555 Dihedral : 4.903 26.418 10095 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.43 % Allowed : 13.03 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.09), residues: 9345 helix: 1.28 (0.08), residues: 5060 sheet: -1.20 (0.24), residues: 475 loop : -2.60 (0.09), residues: 3810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 336 HIS 0.006 0.001 HIS E1095 PHE 0.015 0.001 PHE C1308 TYR 0.014 0.001 TYR A1484 ARG 0.009 0.000 ARG A1628 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 768 time to evaluate : 6.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7352 (t) REVERT: A 671 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.5014 (mmm) REVERT: A 1527 MET cc_start: 0.6899 (mtm) cc_final: 0.6671 (mtm) REVERT: A 2012 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8363 (tp) REVERT: B 231 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7374 (t) REVERT: B 300 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7676 (m-40) REVERT: B 432 GLN cc_start: 0.8356 (tp40) cc_final: 0.8034 (pt0) REVERT: B 677 LEU cc_start: 0.8178 (mt) cc_final: 0.7919 (mp) REVERT: B 934 TYR cc_start: 0.6994 (m-80) cc_final: 0.6559 (m-10) REVERT: B 954 TYR cc_start: 0.8008 (m-10) cc_final: 0.7652 (m-80) REVERT: B 1072 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7504 (mpp80) REVERT: B 1878 MET cc_start: 0.5951 (mmp) cc_final: 0.5554 (mmm) REVERT: B 2012 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8197 (tp) REVERT: C 231 SER cc_start: 0.7812 (OUTLIER) cc_final: 0.7375 (t) REVERT: C 432 GLN cc_start: 0.8384 (tp40) cc_final: 0.8067 (pt0) REVERT: C 648 MET cc_start: 0.7985 (tmm) cc_final: 0.7455 (tmm) REVERT: C 677 LEU cc_start: 0.8132 (mt) cc_final: 0.7897 (mp) REVERT: C 714 TRP cc_start: 0.7328 (OUTLIER) cc_final: 0.5979 (t60) REVERT: C 845 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6954 (tm-30) REVERT: C 849 ASP cc_start: 0.8318 (m-30) cc_final: 0.7798 (m-30) REVERT: C 954 TYR cc_start: 0.8130 (m-10) cc_final: 0.7893 (m-80) REVERT: C 1532 THR cc_start: 0.7103 (t) cc_final: 0.6873 (m) REVERT: C 2012 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8248 (tp) REVERT: D 231 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7304 (t) REVERT: D 300 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7513 (m110) REVERT: D 414 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: D 432 GLN cc_start: 0.8347 (tp40) cc_final: 0.8063 (pt0) REVERT: D 492 PHE cc_start: 0.7310 (m-80) cc_final: 0.7076 (m-80) REVERT: D 559 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6711 (pp20) REVERT: D 594 PHE cc_start: 0.8152 (t80) cc_final: 0.7905 (t80) REVERT: D 613 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: D 696 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7363 (mp0) REVERT: D 918 ILE cc_start: 0.7961 (mt) cc_final: 0.7707 (tp) REVERT: D 1399 MET cc_start: 0.7761 (mtm) cc_final: 0.7260 (mtt) REVERT: D 1403 ASP cc_start: 0.7142 (m-30) cc_final: 0.6851 (m-30) REVERT: D 1878 MET cc_start: 0.6046 (mmp) cc_final: 0.5673 (mmm) REVERT: D 2012 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8494 (tp) REVERT: E 231 SER cc_start: 0.7910 (OUTLIER) cc_final: 0.7449 (t) REVERT: E 497 ASN cc_start: 0.8464 (m110) cc_final: 0.8254 (m-40) REVERT: E 822 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7988 (pm20) REVERT: E 934 TYR cc_start: 0.6901 (m-10) cc_final: 0.6548 (m-10) REVERT: E 1269 LEU cc_start: 0.8191 (tp) cc_final: 0.7863 (mp) REVERT: E 1327 ASP cc_start: 0.6761 (OUTLIER) cc_final: 0.6352 (m-30) REVERT: E 1756 TYR cc_start: 0.8772 (t80) cc_final: 0.8298 (t80) REVERT: E 1878 MET cc_start: 0.5976 (mmp) cc_final: 0.5685 (mmm) REVERT: E 2012 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8207 (tp) outliers start: 201 outliers final: 115 residues processed: 920 average time/residue: 0.6940 time to fit residues: 1111.9821 Evaluate side-chains 811 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 677 time to evaluate : 6.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 GLN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1707 GLU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 926 ASN Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1642 VAL Chi-restraints excluded: chain B residue 1768 LEU Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1886 THR Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 714 TRP Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 926 ASN Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1642 VAL Chi-restraints excluded: chain C residue 1644 ILE Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1886 THR Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2027 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 613 GLN Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 926 ASN Chi-restraints excluded: chain D residue 977 SER Chi-restraints excluded: chain D residue 1055 ILE Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1294 LEU Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1707 GLU Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1808 ASP Chi-restraints excluded: chain D residue 1886 THR Chi-restraints excluded: chain D residue 2012 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 597 CYS Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 926 ASN Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 1027 GLN Chi-restraints excluded: chain E residue 1055 ILE Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1327 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1445 HIS Chi-restraints excluded: chain E residue 1534 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1808 ASP Chi-restraints excluded: chain E residue 1886 THR Chi-restraints excluded: chain E residue 2012 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 304 optimal weight: 3.9990 chunk 813 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 chunk 530 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 904 optimal weight: 5.9990 chunk 750 optimal weight: 4.9990 chunk 418 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 299 optimal weight: 5.9990 chunk 474 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS A 989 GLN ** A1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN B 533 HIS ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 HIS ** B1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1433 GLN B1770 ASN B1788 GLN C 490 ASN C 802 HIS ** C 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1408 GLN ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1684 GLN ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1770 ASN C1858 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1770 ASN ** E 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 802 HIS E1770 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 76915 Z= 0.336 Angle : 0.649 12.231 104180 Z= 0.329 Chirality : 0.043 0.263 11525 Planarity : 0.004 0.053 13555 Dihedral : 5.182 26.383 10095 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 2.97 % Allowed : 13.14 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.09), residues: 9345 helix: 1.19 (0.08), residues: 5075 sheet: -1.32 (0.22), residues: 555 loop : -2.60 (0.10), residues: 3715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C1077 HIS 0.009 0.001 HIS D1751 PHE 0.016 0.002 PHE C1976 TYR 0.021 0.002 TYR A1820 ARG 0.010 0.001 ARG B1628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 719 time to evaluate : 6.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7283 (t) REVERT: A 382 MET cc_start: 0.7921 (mmm) cc_final: 0.7719 (mmm) REVERT: A 588 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.9003 (mp) REVERT: A 2012 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8433 (tp) REVERT: B 231 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.7353 (t) REVERT: B 300 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7595 (m-40) REVERT: B 677 LEU cc_start: 0.8125 (mt) cc_final: 0.7853 (mp) REVERT: B 918 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8041 (tp) REVERT: B 934 TYR cc_start: 0.7075 (m-80) cc_final: 0.6800 (m-80) REVERT: B 954 TYR cc_start: 0.8168 (m-10) cc_final: 0.7819 (m-80) REVERT: B 1072 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7677 (mpp80) REVERT: B 2012 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8205 (tp) REVERT: C 231 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7364 (t) REVERT: C 648 MET cc_start: 0.7957 (tmm) cc_final: 0.7653 (tmm) REVERT: C 845 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7127 (tm-30) REVERT: C 849 ASP cc_start: 0.8324 (m-30) cc_final: 0.7953 (m-30) REVERT: C 954 TYR cc_start: 0.8170 (m-10) cc_final: 0.7907 (m-80) REVERT: C 2012 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8281 (tp) REVERT: D 231 SER cc_start: 0.7820 (OUTLIER) cc_final: 0.7324 (t) REVERT: D 300 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7493 (m110) REVERT: D 414 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: D 559 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6756 (pp20) REVERT: D 613 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: D 696 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7390 (mp0) REVERT: D 1399 MET cc_start: 0.7766 (mtm) cc_final: 0.7271 (mtt) REVERT: D 1403 ASP cc_start: 0.7151 (m-30) cc_final: 0.6864 (m-30) REVERT: D 2012 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8519 (tp) REVERT: E 173 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.7008 (tt) REVERT: E 231 SER cc_start: 0.7926 (OUTLIER) cc_final: 0.7366 (t) REVERT: E 822 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7982 (pm20) REVERT: E 934 TYR cc_start: 0.7013 (m-10) cc_final: 0.6678 (m-10) REVERT: E 954 TYR cc_start: 0.8140 (m-10) cc_final: 0.7844 (m-80) REVERT: E 2012 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8224 (tp) outliers start: 246 outliers final: 160 residues processed: 904 average time/residue: 0.7302 time to fit residues: 1165.8347 Evaluate side-chains 836 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 657 time to evaluate : 6.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 GLN Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1572 LEU Chi-restraints excluded: chain A residue 1615 LYS Chi-restraints excluded: chain A residue 1627 SER Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2027 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 772 MET Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1027 GLN Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1076 ASP Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1416 LEU Chi-restraints excluded: chain B residue 1534 LEU Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1642 VAL Chi-restraints excluded: chain B residue 1644 ILE Chi-restraints excluded: chain B residue 1739 GLN Chi-restraints excluded: chain B residue 1768 LEU Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1886 THR Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain B residue 2027 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 745 ILE Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain C residue 926 ASN Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1103 ASP Chi-restraints excluded: chain C residue 1269 LEU Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1570 MET Chi-restraints excluded: chain C residue 1627 SER Chi-restraints excluded: chain C residue 1642 VAL Chi-restraints excluded: chain C residue 1644 ILE Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1808 ASP Chi-restraints excluded: chain C residue 1886 THR Chi-restraints excluded: chain C residue 1937 LEU Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2027 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 613 GLN Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 926 ASN Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 977 SER Chi-restraints excluded: chain D residue 1055 ILE Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1076 ASP Chi-restraints excluded: chain D residue 1133 PHE Chi-restraints excluded: chain D residue 1294 LEU Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1579 GLN Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1808 ASP Chi-restraints excluded: chain D residue 1886 THR Chi-restraints excluded: chain D residue 2012 LEU Chi-restraints excluded: chain D residue 2027 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 886 VAL Chi-restraints excluded: chain E residue 926 ASN Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 1055 ILE Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1076 ASP Chi-restraints excluded: chain E residue 1103 ASP Chi-restraints excluded: chain E residue 1327 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1445 HIS Chi-restraints excluded: chain E residue 1534 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1627 SER Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1808 ASP Chi-restraints excluded: chain E residue 1886 THR Chi-restraints excluded: chain E residue 1937 LEU Chi-restraints excluded: chain E residue 2012 LEU Chi-restraints excluded: chain E residue 2027 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 872 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 515 optimal weight: 3.9990 chunk 660 optimal weight: 0.8980 chunk 511 optimal weight: 0.2980 chunk 761 optimal weight: 2.9990 chunk 505 optimal weight: 5.9990 chunk 901 optimal weight: 3.9990 chunk 563 optimal weight: 8.9990 chunk 549 optimal weight: 2.9990 chunk 416 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN ** A1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 ASN A1977 GLN B 490 ASN B 713 ASN ** B1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1977 GLN ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 ASN ** C 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1977 GLN D 713 ASN ** D 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1977 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 76915 Z= 0.169 Angle : 0.572 11.638 104180 Z= 0.289 Chirality : 0.040 0.267 11525 Planarity : 0.004 0.052 13555 Dihedral : 4.901 26.686 10095 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.28 % Allowed : 14.40 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.09), residues: 9345 helix: 1.53 (0.08), residues: 5045 sheet: -1.26 (0.22), residues: 550 loop : -2.55 (0.10), residues: 3750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 336 HIS 0.007 0.001 HIS E1095 PHE 0.016 0.001 PHE A 747 TYR 0.019 0.001 TYR B1484 ARG 0.009 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 709 time to evaluate : 6.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7276 (t) REVERT: A 300 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7283 (m-40) REVERT: A 2012 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8413 (tp) REVERT: B 231 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7359 (t) REVERT: B 300 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7533 (m-40) REVERT: B 589 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7966 (mttt) REVERT: B 677 LEU cc_start: 0.8106 (mt) cc_final: 0.7848 (mp) REVERT: B 918 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8069 (tp) REVERT: B 934 TYR cc_start: 0.7014 (m-80) cc_final: 0.6611 (m-10) REVERT: B 948 MET cc_start: 0.8116 (mmm) cc_final: 0.7899 (mmm) REVERT: B 954 TYR cc_start: 0.8144 (m-10) cc_final: 0.7749 (m-80) REVERT: B 1072 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7536 (mpp80) REVERT: B 1110 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7998 (m-40) REVERT: B 2012 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8200 (tp) REVERT: C 231 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7337 (t) REVERT: C 648 MET cc_start: 0.7945 (tmm) cc_final: 0.7559 (tmm) REVERT: C 845 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7142 (tm-30) REVERT: C 849 ASP cc_start: 0.8302 (m-30) cc_final: 0.7965 (m-30) REVERT: C 954 TYR cc_start: 0.8181 (m-10) cc_final: 0.7939 (m-80) REVERT: C 2012 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8271 (tp) REVERT: D 231 SER cc_start: 0.7756 (OUTLIER) cc_final: 0.7293 (t) REVERT: D 254 TRP cc_start: 0.7516 (t-100) cc_final: 0.7233 (t-100) REVERT: D 300 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7436 (m-40) REVERT: D 414 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: D 432 GLN cc_start: 0.8355 (tp40) cc_final: 0.8121 (pt0) REVERT: D 559 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6742 (pp20) REVERT: D 696 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7362 (mp0) REVERT: D 918 ILE cc_start: 0.8090 (mt) cc_final: 0.7814 (tp) REVERT: D 1399 MET cc_start: 0.7699 (mtm) cc_final: 0.7244 (mtt) REVERT: D 1403 ASP cc_start: 0.7156 (m-30) cc_final: 0.6875 (m-30) REVERT: D 1878 MET cc_start: 0.6100 (mmp) cc_final: 0.5720 (mmm) REVERT: D 1941 TYR cc_start: 0.6774 (m-80) cc_final: 0.6549 (m-80) REVERT: D 2012 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8491 (tp) REVERT: E 231 SER cc_start: 0.7876 (OUTLIER) cc_final: 0.7386 (t) REVERT: E 677 LEU cc_start: 0.8074 (mt) cc_final: 0.7855 (mp) REVERT: E 738 ILE cc_start: 0.8691 (mt) cc_final: 0.8440 (mt) REVERT: E 822 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7982 (pm20) REVERT: E 918 ILE cc_start: 0.8480 (mm) cc_final: 0.7794 (tp) REVERT: E 934 TYR cc_start: 0.6922 (m-10) cc_final: 0.6606 (m-10) REVERT: E 954 TYR cc_start: 0.8141 (m-10) cc_final: 0.7796 (m-80) REVERT: E 1327 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6370 (m-30) REVERT: E 1878 MET cc_start: 0.6014 (mmp) cc_final: 0.5715 (mmm) REVERT: E 2012 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8210 (tp) outliers start: 189 outliers final: 138 residues processed: 843 average time/residue: 0.6773 time to fit residues: 1003.8952 Evaluate side-chains 813 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 656 time to evaluate : 6.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 GLN Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1572 LEU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1707 GLU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 708 GLN Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 926 ASN Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1416 LEU Chi-restraints excluded: chain B residue 1534 LEU Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1642 VAL Chi-restraints excluded: chain B residue 1644 ILE Chi-restraints excluded: chain B residue 1739 GLN Chi-restraints excluded: chain B residue 1768 LEU Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1886 THR Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain B residue 2027 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain C residue 745 ILE Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 926 ASN Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1103 ASP Chi-restraints excluded: chain C residue 1269 LEU Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1570 MET Chi-restraints excluded: chain C residue 1642 VAL Chi-restraints excluded: chain C residue 1644 ILE Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1886 THR Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2027 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 926 ASN Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1055 ILE Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1294 LEU Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1408 GLN Chi-restraints excluded: chain D residue 1490 LEU Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1627 SER Chi-restraints excluded: chain D residue 1707 GLU Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1808 ASP Chi-restraints excluded: chain D residue 1886 THR Chi-restraints excluded: chain D residue 1937 LEU Chi-restraints excluded: chain D residue 2012 LEU Chi-restraints excluded: chain D residue 2027 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 926 ASN Chi-restraints excluded: chain E residue 955 ILE Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 1055 ILE Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1103 ASP Chi-restraints excluded: chain E residue 1327 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1445 HIS Chi-restraints excluded: chain E residue 1534 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1627 SER Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1808 ASP Chi-restraints excluded: chain E residue 1886 THR Chi-restraints excluded: chain E residue 2012 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 557 optimal weight: 1.9990 chunk 359 optimal weight: 4.9990 chunk 538 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 572 optimal weight: 7.9990 chunk 613 optimal weight: 0.0040 chunk 445 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 708 optimal weight: 0.5980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1515 HIS ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 ASN ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1684 GLN ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 76915 Z= 0.169 Angle : 0.568 11.517 104180 Z= 0.286 Chirality : 0.040 0.276 11525 Planarity : 0.004 0.048 13555 Dihedral : 4.752 26.137 10095 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.19 % Allowed : 14.61 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.09), residues: 9345 helix: 1.67 (0.08), residues: 5045 sheet: -1.16 (0.22), residues: 550 loop : -2.49 (0.10), residues: 3750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 336 HIS 0.006 0.001 HIS E 165 PHE 0.023 0.001 PHE D 747 TYR 0.017 0.001 TYR B1484 ARG 0.010 0.000 ARG E 635 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 687 time to evaluate : 6.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7302 (t) REVERT: A 708 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: A 2012 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8395 (tp) REVERT: B 231 SER cc_start: 0.7771 (OUTLIER) cc_final: 0.7350 (t) REVERT: B 254 TRP cc_start: 0.7438 (t-100) cc_final: 0.7197 (t-100) REVERT: B 300 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7520 (m-40) REVERT: B 589 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7921 (mttt) REVERT: B 677 LEU cc_start: 0.8071 (mt) cc_final: 0.7809 (mp) REVERT: B 918 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8106 (tp) REVERT: B 934 TYR cc_start: 0.6983 (m-80) cc_final: 0.6595 (m-10) REVERT: B 954 TYR cc_start: 0.8123 (m-10) cc_final: 0.7754 (m-80) REVERT: B 1072 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7540 (mpp80) REVERT: B 1110 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8028 (m-40) REVERT: B 2012 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8180 (tp) REVERT: C 231 SER cc_start: 0.7815 (OUTLIER) cc_final: 0.7385 (t) REVERT: C 648 MET cc_start: 0.7943 (tmm) cc_final: 0.7655 (tmm) REVERT: C 845 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7114 (tm-30) REVERT: C 849 ASP cc_start: 0.8296 (m-30) cc_final: 0.7947 (m-30) REVERT: C 954 TYR cc_start: 0.8172 (m-10) cc_final: 0.7953 (m-80) REVERT: C 1767 GLU cc_start: 0.7695 (tt0) cc_final: 0.7203 (tt0) REVERT: C 2012 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8245 (tp) REVERT: D 231 SER cc_start: 0.7722 (OUTLIER) cc_final: 0.7273 (t) REVERT: D 254 TRP cc_start: 0.7513 (t-100) cc_final: 0.7256 (t-100) REVERT: D 300 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7355 (m-40) REVERT: D 432 GLN cc_start: 0.8343 (tp40) cc_final: 0.8118 (pt0) REVERT: D 696 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7354 (mp0) REVERT: D 1399 MET cc_start: 0.7689 (mtm) cc_final: 0.7232 (mtt) REVERT: D 1403 ASP cc_start: 0.7153 (m-30) cc_final: 0.6870 (m-30) REVERT: D 1534 LEU cc_start: 0.8431 (pp) cc_final: 0.8222 (tt) REVERT: D 1878 MET cc_start: 0.6145 (mmp) cc_final: 0.5777 (mmm) REVERT: D 1941 TYR cc_start: 0.6824 (m-80) cc_final: 0.6619 (m-80) REVERT: D 2012 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8475 (tp) REVERT: E 231 SER cc_start: 0.7932 (OUTLIER) cc_final: 0.7442 (t) REVERT: E 677 LEU cc_start: 0.8112 (mt) cc_final: 0.7897 (mp) REVERT: E 738 ILE cc_start: 0.8705 (mt) cc_final: 0.8450 (mt) REVERT: E 822 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7996 (pm20) REVERT: E 918 ILE cc_start: 0.8529 (mm) cc_final: 0.7882 (tp) REVERT: E 934 TYR cc_start: 0.6880 (m-10) cc_final: 0.6592 (m-10) REVERT: E 954 TYR cc_start: 0.8157 (m-10) cc_final: 0.7845 (m-80) REVERT: E 1878 MET cc_start: 0.6035 (mmp) cc_final: 0.5759 (mmm) REVERT: E 2012 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8205 (tp) outliers start: 181 outliers final: 139 residues processed: 813 average time/residue: 0.6796 time to fit residues: 969.1999 Evaluate side-chains 802 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 647 time to evaluate : 6.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 GLN Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1572 LEU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1707 GLU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2027 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 708 GLN Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 926 ASN Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1416 LEU Chi-restraints excluded: chain B residue 1534 LEU Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1642 VAL Chi-restraints excluded: chain B residue 1644 ILE Chi-restraints excluded: chain B residue 1739 GLN Chi-restraints excluded: chain B residue 1768 LEU Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1886 THR Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain B residue 2027 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 714 TRP Chi-restraints excluded: chain C residue 745 ILE Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 926 ASN Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1103 ASP Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1570 MET Chi-restraints excluded: chain C residue 1642 VAL Chi-restraints excluded: chain C residue 1644 ILE Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1808 ASP Chi-restraints excluded: chain C residue 1886 THR Chi-restraints excluded: chain C residue 1937 LEU Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2027 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 926 ASN Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1055 ILE Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1294 LEU Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1642 VAL Chi-restraints excluded: chain D residue 1707 GLU Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1808 ASP Chi-restraints excluded: chain D residue 1886 THR Chi-restraints excluded: chain D residue 1937 LEU Chi-restraints excluded: chain D residue 2012 LEU Chi-restraints excluded: chain D residue 2027 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 597 CYS Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 926 ASN Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 1055 ILE Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1103 ASP Chi-restraints excluded: chain E residue 1327 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1445 HIS Chi-restraints excluded: chain E residue 1534 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1627 SER Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1808 ASP Chi-restraints excluded: chain E residue 1886 THR Chi-restraints excluded: chain E residue 2012 LEU Chi-restraints excluded: chain E residue 2027 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 819 optimal weight: 5.9990 chunk 863 optimal weight: 0.8980 chunk 787 optimal weight: 0.1980 chunk 839 optimal weight: 0.6980 chunk 505 optimal weight: 0.9990 chunk 365 optimal weight: 9.9990 chunk 659 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 chunk 758 optimal weight: 0.8980 chunk 794 optimal weight: 2.9990 chunk 836 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 GLN ** C 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 GLN E1488 HIS ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 76915 Z= 0.158 Angle : 0.557 11.564 104180 Z= 0.281 Chirality : 0.039 0.277 11525 Planarity : 0.004 0.048 13555 Dihedral : 4.659 26.033 10095 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 2.01 % Allowed : 14.92 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.09), residues: 9345 helix: 1.78 (0.08), residues: 5040 sheet: -1.10 (0.22), residues: 550 loop : -2.47 (0.10), residues: 3755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 336 HIS 0.006 0.001 HIS B1095 PHE 0.015 0.001 PHE A 747 TYR 0.018 0.001 TYR E1484 ARG 0.011 0.000 ARG B1813 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 696 time to evaluate : 6.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.7798 (OUTLIER) cc_final: 0.7359 (t) REVERT: A 708 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: A 2012 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8367 (tp) REVERT: B 231 SER cc_start: 0.7719 (OUTLIER) cc_final: 0.7322 (t) REVERT: B 254 TRP cc_start: 0.7395 (t-100) cc_final: 0.7179 (t-100) REVERT: B 300 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7513 (m-40) REVERT: B 589 LYS cc_start: 0.8246 (mtmt) cc_final: 0.7920 (mttt) REVERT: B 677 LEU cc_start: 0.8059 (mt) cc_final: 0.7800 (mp) REVERT: B 918 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8117 (tp) REVERT: B 934 TYR cc_start: 0.6952 (m-80) cc_final: 0.6561 (m-10) REVERT: B 954 TYR cc_start: 0.8107 (m-10) cc_final: 0.7753 (m-80) REVERT: B 1072 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7497 (mpp80) REVERT: B 1110 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7985 (m-40) REVERT: B 1878 MET cc_start: 0.6031 (mmp) cc_final: 0.5733 (mmm) REVERT: B 2012 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8154 (tp) REVERT: C 231 SER cc_start: 0.7820 (OUTLIER) cc_final: 0.7386 (t) REVERT: C 648 MET cc_start: 0.7929 (tmm) cc_final: 0.7628 (tmm) REVERT: C 714 TRP cc_start: 0.7497 (OUTLIER) cc_final: 0.5626 (t60) REVERT: C 845 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6980 (tm-30) REVERT: C 849 ASP cc_start: 0.8278 (m-30) cc_final: 0.7764 (m-30) REVERT: C 954 TYR cc_start: 0.8161 (m-10) cc_final: 0.7915 (m-80) REVERT: D 231 SER cc_start: 0.7709 (OUTLIER) cc_final: 0.7277 (t) REVERT: D 254 TRP cc_start: 0.7495 (t-100) cc_final: 0.7270 (t-100) REVERT: D 300 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7374 (m-40) REVERT: D 401 TYR cc_start: 0.7628 (m-80) cc_final: 0.7364 (m-80) REVERT: D 492 PHE cc_start: 0.7331 (m-80) cc_final: 0.7091 (m-80) REVERT: D 918 ILE cc_start: 0.8066 (mt) cc_final: 0.7814 (tp) REVERT: D 1399 MET cc_start: 0.7677 (mtm) cc_final: 0.7227 (mtt) REVERT: D 1403 ASP cc_start: 0.7167 (m-30) cc_final: 0.6877 (m-30) REVERT: D 1534 LEU cc_start: 0.8438 (pp) cc_final: 0.8223 (tt) REVERT: D 1878 MET cc_start: 0.6120 (mmp) cc_final: 0.5809 (mmm) REVERT: D 2012 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8466 (tp) REVERT: E 231 SER cc_start: 0.7901 (OUTLIER) cc_final: 0.7419 (t) REVERT: E 677 LEU cc_start: 0.8111 (mt) cc_final: 0.7896 (mp) REVERT: E 738 ILE cc_start: 0.8701 (mt) cc_final: 0.8441 (mt) REVERT: E 822 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7978 (pm20) REVERT: E 918 ILE cc_start: 0.8541 (mm) cc_final: 0.7902 (tp) REVERT: E 934 TYR cc_start: 0.6865 (m-10) cc_final: 0.6576 (m-10) REVERT: E 954 TYR cc_start: 0.8168 (m-10) cc_final: 0.7856 (m-80) REVERT: E 1291 LYS cc_start: 0.8579 (mttm) cc_final: 0.8375 (mtmm) REVERT: E 1878 MET cc_start: 0.6030 (mmp) cc_final: 0.5773 (mmm) REVERT: E 2012 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8211 (tp) outliers start: 166 outliers final: 139 residues processed: 811 average time/residue: 0.6822 time to fit residues: 969.6859 Evaluate side-chains 809 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 654 time to evaluate : 6.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 GLN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1572 LEU Chi-restraints excluded: chain A residue 1707 GLU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2027 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 708 GLN Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 926 ASN Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1416 LEU Chi-restraints excluded: chain B residue 1534 LEU Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1642 VAL Chi-restraints excluded: chain B residue 1739 GLN Chi-restraints excluded: chain B residue 1768 LEU Chi-restraints excluded: chain B residue 1886 THR Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain B residue 2027 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 714 TRP Chi-restraints excluded: chain C residue 745 ILE Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain C residue 926 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1103 ASP Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1570 MET Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1808 ASP Chi-restraints excluded: chain C residue 1886 THR Chi-restraints excluded: chain C residue 2027 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 926 ASN Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1055 ILE Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1294 LEU Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1408 GLN Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1642 VAL Chi-restraints excluded: chain D residue 1707 GLU Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1886 THR Chi-restraints excluded: chain D residue 1937 LEU Chi-restraints excluded: chain D residue 2012 LEU Chi-restraints excluded: chain D residue 2027 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 597 CYS Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 886 VAL Chi-restraints excluded: chain E residue 926 ASN Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 1055 ILE Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1103 ASP Chi-restraints excluded: chain E residue 1327 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1445 HIS Chi-restraints excluded: chain E residue 1534 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1627 SER Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1808 ASP Chi-restraints excluded: chain E residue 1886 THR Chi-restraints excluded: chain E residue 1937 LEU Chi-restraints excluded: chain E residue 2012 LEU Chi-restraints excluded: chain E residue 2027 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 551 optimal weight: 4.9990 chunk 888 optimal weight: 0.7980 chunk 542 optimal weight: 6.9990 chunk 421 optimal weight: 2.9990 chunk 617 optimal weight: 10.0000 chunk 931 optimal weight: 8.9990 chunk 857 optimal weight: 0.5980 chunk 741 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 572 optimal weight: 6.9990 chunk 454 optimal weight: 0.0170 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 ASN ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 76915 Z= 0.196 Angle : 0.573 11.038 104180 Z= 0.290 Chirality : 0.040 0.266 11525 Planarity : 0.004 0.048 13555 Dihedral : 4.689 25.909 10095 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.02 % Allowed : 15.12 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.09), residues: 9345 helix: 1.78 (0.08), residues: 5040 sheet: -1.06 (0.22), residues: 550 loop : -2.45 (0.10), residues: 3755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 254 HIS 0.006 0.001 HIS E1095 PHE 0.020 0.001 PHE D 747 TYR 0.019 0.001 TYR E1484 ARG 0.009 0.000 ARG A1628 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18690 Ramachandran restraints generated. 9345 Oldfield, 0 Emsley, 9345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 674 time to evaluate : 6.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.7815 (OUTLIER) cc_final: 0.7372 (t) REVERT: A 708 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: B 231 SER cc_start: 0.7731 (OUTLIER) cc_final: 0.7325 (t) REVERT: B 254 TRP cc_start: 0.7377 (t-100) cc_final: 0.7173 (t-100) REVERT: B 300 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7496 (m-40) REVERT: B 380 MET cc_start: 0.8194 (mtm) cc_final: 0.7879 (mtm) REVERT: B 589 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7898 (mttt) REVERT: B 677 LEU cc_start: 0.8060 (mt) cc_final: 0.7804 (mp) REVERT: B 918 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8150 (tp) REVERT: B 934 TYR cc_start: 0.6998 (m-80) cc_final: 0.6622 (m-10) REVERT: B 954 TYR cc_start: 0.8147 (m-10) cc_final: 0.7804 (m-80) REVERT: B 1072 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7547 (mpp80) REVERT: B 1110 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8021 (m-40) REVERT: B 1878 MET cc_start: 0.6046 (mmp) cc_final: 0.5736 (mmm) REVERT: B 2012 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8151 (tp) REVERT: C 231 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7377 (t) REVERT: C 648 MET cc_start: 0.7918 (tmm) cc_final: 0.7584 (tmm) REVERT: C 714 TRP cc_start: 0.7481 (OUTLIER) cc_final: 0.5555 (t60) REVERT: C 845 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7114 (tm-30) REVERT: C 849 ASP cc_start: 0.8277 (m-30) cc_final: 0.7927 (m-30) REVERT: C 954 TYR cc_start: 0.8197 (m-10) cc_final: 0.7945 (m-80) REVERT: D 231 SER cc_start: 0.7724 (OUTLIER) cc_final: 0.7279 (t) REVERT: D 300 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7380 (m-40) REVERT: D 401 TYR cc_start: 0.7725 (m-80) cc_final: 0.7343 (m-80) REVERT: D 559 GLU cc_start: 0.7491 (pm20) cc_final: 0.7277 (pm20) REVERT: D 1399 MET cc_start: 0.7688 (mtm) cc_final: 0.7244 (mtt) REVERT: D 1403 ASP cc_start: 0.7165 (m-30) cc_final: 0.6874 (m-30) REVERT: D 1878 MET cc_start: 0.6131 (mmp) cc_final: 0.5823 (mmm) REVERT: D 2012 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8459 (tp) REVERT: E 231 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7427 (t) REVERT: E 677 LEU cc_start: 0.8139 (mt) cc_final: 0.7926 (mp) REVERT: E 738 ILE cc_start: 0.8712 (mt) cc_final: 0.8510 (mt) REVERT: E 822 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7976 (pm20) REVERT: E 918 ILE cc_start: 0.8544 (mm) cc_final: 0.7906 (tp) REVERT: E 934 TYR cc_start: 0.6876 (m-10) cc_final: 0.6587 (m-10) REVERT: E 954 TYR cc_start: 0.8205 (m-10) cc_final: 0.7900 (m-80) REVERT: E 1291 LYS cc_start: 0.8627 (mttm) cc_final: 0.8409 (mtmm) REVERT: E 1878 MET cc_start: 0.6047 (mmp) cc_final: 0.5784 (mmm) REVERT: E 2012 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8203 (tp) outliers start: 167 outliers final: 145 residues processed: 793 average time/residue: 0.6713 time to fit residues: 938.4453 Evaluate side-chains 803 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 643 time to evaluate : 6.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1133 PHE Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 GLN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1572 LEU Chi-restraints excluded: chain A residue 1707 GLU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 2027 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 708 GLN Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain B residue 926 ASN Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1416 LEU Chi-restraints excluded: chain B residue 1534 LEU Chi-restraints excluded: chain B residue 1539 LEU Chi-restraints excluded: chain B residue 1627 SER Chi-restraints excluded: chain B residue 1642 VAL Chi-restraints excluded: chain B residue 1739 GLN Chi-restraints excluded: chain B residue 1768 LEU Chi-restraints excluded: chain B residue 1886 THR Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain B residue 2027 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 714 TRP Chi-restraints excluded: chain C residue 745 ILE Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain C residue 926 ASN Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 1055 ILE Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1103 ASP Chi-restraints excluded: chain C residue 1269 LEU Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1570 MET Chi-restraints excluded: chain C residue 1644 ILE Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1808 ASP Chi-restraints excluded: chain C residue 1886 THR Chi-restraints excluded: chain C residue 1937 LEU Chi-restraints excluded: chain C residue 2027 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 714 TRP Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 926 ASN Chi-restraints excluded: chain D residue 1055 ILE Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1294 LEU Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1408 GLN Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1642 VAL Chi-restraints excluded: chain D residue 1707 GLU Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1886 THR Chi-restraints excluded: chain D residue 1937 LEU Chi-restraints excluded: chain D residue 2012 LEU Chi-restraints excluded: chain D residue 2027 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 597 CYS Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 714 TRP Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 772 MET Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 886 VAL Chi-restraints excluded: chain E residue 926 ASN Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 1055 ILE Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1103 ASP Chi-restraints excluded: chain E residue 1327 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1445 HIS Chi-restraints excluded: chain E residue 1534 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1627 SER Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1808 ASP Chi-restraints excluded: chain E residue 1886 THR Chi-restraints excluded: chain E residue 1937 LEU Chi-restraints excluded: chain E residue 2012 LEU Chi-restraints excluded: chain E residue 2027 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 589 optimal weight: 8.9990 chunk 790 optimal weight: 0.7980 chunk 227 optimal weight: 0.0870 chunk 683 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 742 optimal weight: 9.9990 chunk 310 optimal weight: 1.9990 chunk 762 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 989 GLN ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.132880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.104738 restraints weight = 131966.961| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.55 r_work: 0.3221 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 76915 Z= 0.160 Angle : 0.556 10.671 104180 Z= 0.281 Chirality : 0.039 0.262 11525 Planarity : 0.004 0.047 13555 Dihedral : 4.583 25.951 10095 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.92 % Allowed : 15.37 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.09), residues: 9345 helix: 1.89 (0.08), residues: 5040 sheet: -1.02 (0.23), residues: 550 loop : -2.44 (0.10), residues: 3755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 336 HIS 0.006 0.001 HIS B1095 PHE 0.011 0.001 PHE E1133 TYR 0.020 0.001 TYR E1484 ARG 0.011 0.000 ARG B 635 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21471.97 seconds wall clock time: 370 minutes 27.93 seconds (22227.93 seconds total)