Starting phenix.real_space_refine on Sat Mar 16 22:31:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwb_10037/03_2024/6rwb_10037.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwb_10037/03_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_10037/03_2024/6rwb_10037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwb_10037/03_2024/6rwb_10037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwb_10037/03_2024/6rwb_10037.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwb_10037/03_2024/6rwb_10037.pdb" } 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 Residue "A ARG 194": "NH1" <-> "NH2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1246": "NH1" <-> "NH2" Residue "A ARG 1438": "NH1" <-> "NH2" Residue "A ARG 1457": "NH1" <-> "NH2" Residue "A ARG 1536": "NH1" <-> "NH2" Residue "A ARG 1813": "NH1" <-> "NH2" Residue "A ARG 2002": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "B ARG 1022": "NH1" <-> "NH2" Residue "B TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1246": "NH1" <-> "NH2" Residue "B ARG 1438": "NH1" <-> "NH2" Residue "B ARG 1457": "NH1" <-> "NH2" Residue "B ARG 1536": "NH1" <-> "NH2" Residue "B ARG 1813": "NH1" <-> "NH2" Residue "B ARG 2002": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 379": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "C ARG 1022": "NH1" <-> "NH2" Residue "C TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1246": "NH1" <-> "NH2" Residue "C ARG 1438": "NH1" <-> "NH2" Residue "C ARG 1457": "NH1" <-> "NH2" Residue "C ARG 1536": "NH1" <-> "NH2" Residue "C ARG 1813": "NH1" <-> "NH2" Residue "C ARG 2002": "NH1" <-> "NH2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 379": "NH1" <-> "NH2" Residue "D ARG 577": "NH1" <-> "NH2" Residue "D ARG 635": "NH1" <-> "NH2" Residue "D ARG 766": "NH1" <-> "NH2" Residue "D ARG 1022": "NH1" <-> "NH2" Residue "D TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1246": "NH1" <-> "NH2" Residue "D ARG 1438": "NH1" <-> "NH2" Residue "D ARG 1457": "NH1" <-> "NH2" Residue "D ARG 1536": "NH1" <-> "NH2" Residue "D ARG 1813": "NH1" <-> "NH2" Residue "D ARG 2002": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 379": "NH1" <-> "NH2" Residue "E ARG 577": "NH1" <-> "NH2" Residue "E ARG 635": "NH1" <-> "NH2" Residue "E ARG 766": "NH1" <-> "NH2" Residue "E ARG 1022": "NH1" <-> "NH2" Residue "E TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1246": "NH1" <-> "NH2" Residue "E ARG 1438": "NH1" <-> "NH2" Residue "E ARG 1457": "NH1" <-> "NH2" Residue "E ARG 1536": "NH1" <-> "NH2" Residue "E ARG 1813": "NH1" <-> "NH2" Residue "E ARG 2002": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 75405 Number of models: 1 Model: "" Number of chains: 5 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 Chain: "B" 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Time building chain proxies: 28.54, per 1000 atoms: 0.38 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 - 3.50 Amino acid : False - 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: 23.17 Conformation dependent library (CDL) restraints added in 10.2 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: 5.93 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: 29.64 Time building geometry restraints manager: 25.65 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: 98.39 - 105.52: 1203 105.52 - 112.66: 39426 112.66 - 119.80: 27451 119.80 - 126.93: 35120 126.93 - 134.07: 980 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 2.440 nonbonded pdb=" OH TYR B 452 " pdb=" OE1 GLN B 550 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR E 452 " pdb=" OE1 GLN E 550 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR A 452 " pdb=" OE1 GLN A 550 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR C 452 " pdb=" OE1 GLN C 550 " model vdw 2.254 2.440 ... (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 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: 9.620 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: 0.070 Extract box with map and model: 33.380 Check model and map are aligned: 0.820 Set scattering table: 0.540 Process input model: 154.060 Find NCS groups from input model: 3.580 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.960 ------------------------------------------------------------------------------- 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 : 6.408 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: 0.7936 time to fit residues: 2853.3637 Evaluate side-chains 958 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 948 time to evaluate : 6.473 ------------------------------------------------------------------------------- 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: 0.9980 chunk 393 optimal weight: 0.6980 chunk 242 optimal weight: 6.9990 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: 0.9980 chunk 545 optimal weight: 7.9990 chunk 849 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN ** A 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 989 GLN A1071 ASN A1311 HIS A1408 GLN A1469 ASN ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN A1591 ASN 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 329 ASN B 437 GLN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN B 490 ASN B 509 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 HIS B 823 ASN B 831 ASN B 914 HIS B 921 HIS B1071 ASN B1110 ASN B1311 HIS ** B1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1463 HIS B1469 ASN ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1519 ASN ** B1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1575 GLN B1684 GLN B1788 GLN B1858 GLN ** B1884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN C 490 ASN C 509 ASN C 556 GLN C 598 GLN ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 GLN ** C 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** C1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1575 GLN C1591 ASN C1684 GLN ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1788 GLN C1858 GLN C1884 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN ** D 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 HIS D 823 ASN D 831 ASN D 914 HIS D 921 HIS D1071 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 D1858 GLN ** D1884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 490 ASN E 509 ASN E 556 GLN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 702 GLN ** E 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 792 HIS E 823 ASN E 831 ASN E 914 HIS E 921 HIS E1071 ASN E1110 ASN E1311 HIS ** E1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1469 ASN E1519 ASN E1575 GLN E1591 ASN E1684 GLN E1788 GLN E1858 GLN ** E1884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1954 ASN Total number of N/Q/H flips: 143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 76915 Z= 0.184 Angle : 0.618 12.533 104180 Z= 0.318 Chirality : 0.040 0.213 11525 Planarity : 0.005 0.059 13555 Dihedral : 5.995 59.870 10115 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.19 % Allowed : 9.03 % 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: -2.18 (0.08), residues: 9345 helix: -0.29 (0.07), residues: 5040 sheet: -2.11 (0.22), residues: 465 loop : -2.98 (0.09), residues: 3840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1068 HIS 0.007 0.001 HIS A1095 PHE 0.022 0.002 PHE B1308 TYR 0.018 0.001 TYR C 950 ARG 0.005 0.001 ARG B 635 *********************** 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 1198 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1017 time to evaluate : 6.643 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 300 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7832 (m-40) REVERT: A 401 TYR cc_start: 0.6411 (t80) cc_final: 0.6087 (t80) REVERT: A 671 MET cc_start: 0.5641 (mtp) cc_final: 0.5141 (mmm) REVERT: A 996 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6763 (tt0) REVERT: A 1110 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8269 (m110) REVERT: A 1468 TYR cc_start: 0.6661 (t80) cc_final: 0.5885 (t80) REVERT: A 2012 LEU cc_start: 0.8740 (pp) cc_final: 0.8434 (tp) REVERT: B 300 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7638 (m-40) REVERT: B 401 TYR cc_start: 0.6474 (t80) cc_final: 0.6126 (t80) REVERT: B 414 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: B 432 GLN cc_start: 0.8348 (tp40) cc_final: 0.8131 (pt0) REVERT: B 440 ASP cc_start: 0.6831 (p0) cc_final: 0.6566 (p0) REVERT: B 457 THR cc_start: 0.8148 (p) cc_final: 0.7185 (p) REVERT: B 671 MET cc_start: 0.6534 (mtt) cc_final: 0.6100 (mmm) REVERT: B 696 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7474 (mp0) REVERT: B 934 TYR cc_start: 0.7196 (m-80) cc_final: 0.6852 (m-10) REVERT: B 1468 TYR cc_start: 0.6679 (t80) cc_final: 0.5929 (t80) REVERT: B 1593 ILE cc_start: 0.8895 (pt) cc_final: 0.8336 (mt) REVERT: B 2012 LEU cc_start: 0.8627 (pp) cc_final: 0.8291 (tp) REVERT: C 411 LYS cc_start: 0.8629 (mttt) cc_final: 0.8392 (ptmm) REVERT: C 422 ASP cc_start: 0.7135 (m-30) cc_final: 0.6912 (m-30) REVERT: C 432 GLN cc_start: 0.8400 (tp40) cc_final: 0.8084 (pt0) REVERT: C 648 MET cc_start: 0.7986 (tmm) cc_final: 0.7462 (tmm) REVERT: C 671 MET cc_start: 0.6706 (mtt) cc_final: 0.6231 (mmm) REVERT: C 729 ASP cc_start: 0.7607 (p0) cc_final: 0.7335 (p0) REVERT: C 934 TYR cc_start: 0.7162 (m-80) cc_final: 0.6772 (m-10) REVERT: C 1468 TYR cc_start: 0.6570 (t80) cc_final: 0.5698 (t80) REVERT: C 1626 SER cc_start: 0.8758 (t) cc_final: 0.8225 (p) REVERT: C 2012 LEU cc_start: 0.8588 (pp) cc_final: 0.8273 (tp) REVERT: D 300 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7570 (m-40) REVERT: D 414 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: D 432 GLN cc_start: 0.8358 (tp40) cc_final: 0.8140 (pt0) REVERT: D 457 THR cc_start: 0.8134 (p) cc_final: 0.7146 (p) REVERT: D 671 MET cc_start: 0.6697 (mtt) cc_final: 0.6269 (mmm) REVERT: D 696 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7465 (mp0) REVERT: D 1399 MET cc_start: 0.7737 (mtm) cc_final: 0.6986 (mtt) REVERT: D 1403 ASP cc_start: 0.7086 (m-30) cc_final: 0.6719 (m-30) REVERT: D 1793 MET cc_start: 0.7988 (mtm) cc_final: 0.7729 (mtm) REVERT: D 2012 LEU cc_start: 0.8779 (pp) cc_final: 0.8485 (tp) REVERT: E 300 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7470 (m-40) REVERT: E 414 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: E 422 ASP cc_start: 0.7234 (m-30) cc_final: 0.7013 (m-30) REVERT: E 648 MET cc_start: 0.7773 (tmm) cc_final: 0.7389 (tmm) REVERT: E 671 MET cc_start: 0.6749 (mtt) cc_final: 0.6266 (mmm) REVERT: E 1593 ILE cc_start: 0.8862 (pt) cc_final: 0.8326 (mt) REVERT: E 1756 TYR cc_start: 0.8751 (t80) cc_final: 0.8277 (t80) REVERT: E 2012 LEU cc_start: 0.8643 (pp) cc_final: 0.8308 (tp) outliers start: 181 outliers final: 90 residues processed: 1151 average time/residue: 0.7350 time to fit residues: 1467.1549 Evaluate side-chains 814 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 715 time to evaluate : 6.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 209 THR 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 787 LEU Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1110 ASN 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 1627 SER 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 B residue 112 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 209 THR 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 414 GLN Chi-restraints excluded: chain B residue 435 SER 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 1076 ASP Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1404 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 209 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 435 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 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 D residue 112 ASP Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 203 GLU 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 1064 ILE Chi-restraints excluded: chain D residue 1076 ASP 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 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 209 THR 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 772 MET Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 1027 GLN Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1076 ASP 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: 1.9990 chunk 263 optimal weight: 0.9980 chunk 706 optimal weight: 0.8980 chunk 578 optimal weight: 0.0270 chunk 234 optimal weight: 2.9990 chunk 850 optimal weight: 2.9990 chunk 918 optimal weight: 6.9990 chunk 757 optimal weight: 0.9980 chunk 843 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 682 optimal weight: 5.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- 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 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1330 GLN ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN A1684 GLN A1716 GLN ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 ASN ** B1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1575 GLN B1591 ASN B1716 GLN B1739 GLN B1884 GLN ** B1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN C 333 GLN C 466 ASN C 533 HIS C 539 GLN C 556 GLN ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN ** C 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1365 GLN ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1575 GLN 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 466 ASN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 753 ASN D 976 ASN D1348 ASN D1408 GLN ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1575 GLN D1716 GLN D1739 GLN D1884 GLN ** D1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 GLN E 466 ASN ** E 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 753 ASN ** E 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 976 ASN E1330 GLN E1575 GLN E1716 GLN E1739 GLN ** E1770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1884 GLN ** E1929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 76915 Z= 0.179 Angle : 0.582 11.194 104180 Z= 0.296 Chirality : 0.039 0.231 11525 Planarity : 0.004 0.051 13555 Dihedral : 5.387 47.488 10105 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.33 % Allowed : 11.11 % Favored : 86.56 % 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: -1.33 (0.09), residues: 9345 helix: 0.52 (0.08), residues: 5045 sheet: -1.67 (0.23), residues: 445 loop : -2.79 (0.09), residues: 3855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 505 HIS 0.006 0.001 HIS D1095 PHE 0.015 0.001 PHE B1308 TYR 0.013 0.001 TYR C 950 ARG 0.008 0.000 ARG A 635 *********************** 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 983 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 790 time to evaluate : 6.583 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: 0.7706 (OUTLIER) cc_final: 0.7315 (t) REVERT: A 300 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7786 (m-40) REVERT: A 414 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7759 (mp10) REVERT: A 497 ASN cc_start: 0.8465 (m110) cc_final: 0.8249 (m-40) REVERT: A 671 MET cc_start: 0.5607 (mtp) cc_final: 0.5153 (mmm) REVERT: A 1110 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8136 (m110) REVERT: A 1411 GLN cc_start: 0.8296 (tp40) cc_final: 0.8042 (tp40) REVERT: A 1593 ILE cc_start: 0.8852 (pt) cc_final: 0.8597 (mt) REVERT: A 1626 SER cc_start: 0.8978 (t) cc_final: 0.8698 (p) REVERT: A 2012 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8412 (tp) REVERT: B 231 SER cc_start: 0.7631 (OUTLIER) cc_final: 0.7209 (t) REVERT: B 300 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7699 (m-40) REVERT: B 432 GLN cc_start: 0.8351 (tp40) cc_final: 0.8087 (pt0) REVERT: B 671 MET cc_start: 0.6592 (mtt) cc_final: 0.6133 (mmm) REVERT: B 677 LEU cc_start: 0.8212 (mt) cc_final: 0.7927 (mp) REVERT: B 934 TYR cc_start: 0.7186 (m-80) cc_final: 0.6905 (m-10) REVERT: B 1593 ILE cc_start: 0.8874 (pt) cc_final: 0.8341 (mt) REVERT: B 2012 LEU cc_start: 0.8555 (pp) cc_final: 0.8242 (tp) REVERT: C 231 SER cc_start: 0.7607 (OUTLIER) cc_final: 0.7209 (t) REVERT: C 392 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8533 (p) REVERT: C 411 LYS cc_start: 0.8610 (mttt) cc_final: 0.8376 (ptmm) REVERT: C 432 GLN cc_start: 0.8373 (tp40) cc_final: 0.8102 (pt0) REVERT: C 648 MET cc_start: 0.7983 (tmm) cc_final: 0.7452 (tmm) REVERT: C 671 MET cc_start: 0.6724 (mtt) cc_final: 0.6209 (mmm) REVERT: C 1626 SER cc_start: 0.8957 (t) cc_final: 0.8696 (p) REVERT: C 1878 MET cc_start: 0.5770 (mmp) cc_final: 0.5434 (mmm) REVERT: C 2012 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8280 (tp) REVERT: D 231 SER cc_start: 0.7743 (OUTLIER) cc_final: 0.7332 (t) REVERT: D 300 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7648 (m110) REVERT: D 414 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: D 432 GLN cc_start: 0.8398 (tp40) cc_final: 0.8111 (pt0) REVERT: D 588 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8942 (mp) REVERT: D 671 MET cc_start: 0.6669 (mtt) cc_final: 0.6195 (mmm) REVERT: D 696 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7293 (mp0) REVERT: D 1399 MET cc_start: 0.7743 (mtm) cc_final: 0.7078 (mtt) REVERT: D 1403 ASP cc_start: 0.7107 (m-30) cc_final: 0.6726 (m-30) REVERT: D 1626 SER cc_start: 0.8984 (t) cc_final: 0.8747 (p) REVERT: D 2012 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8482 (tp) REVERT: E 231 SER cc_start: 0.7615 (OUTLIER) cc_final: 0.7146 (t) REVERT: E 300 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7519 (m110) REVERT: E 648 MET cc_start: 0.7769 (tmm) cc_final: 0.7385 (tmm) REVERT: E 671 MET cc_start: 0.6632 (mtt) cc_final: 0.6164 (mmm) REVERT: E 1110 ASN cc_start: 0.8381 (m110) cc_final: 0.8061 (m-40) REVERT: E 1269 LEU cc_start: 0.8126 (tp) cc_final: 0.7798 (mp) REVERT: E 1756 TYR cc_start: 0.8752 (t80) cc_final: 0.8269 (t80) REVERT: E 1878 MET cc_start: 0.5959 (mmp) cc_final: 0.5617 (mmm) REVERT: E 2012 LEU cc_start: 0.8617 (pp) cc_final: 0.8270 (tp) outliers start: 193 outliers final: 113 residues processed: 934 average time/residue: 0.6795 time to fit residues: 1106.2495 Evaluate side-chains 791 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 661 time to evaluate : 6.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 300 ASN 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 435 SER Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 729 ASP 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 1064 ILE Chi-restraints excluded: chain A residue 1110 ASN 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 1615 LYS 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 1919 MET 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 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 352 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 729 ASP 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 958 THR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1539 LEU 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 392 SER Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 483 ASN 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 958 THR Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1269 LEU Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1519 ASN Chi-restraints excluded: chain C residue 1539 LEU 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 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 414 GLN Chi-restraints excluded: chain D residue 435 SER 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 729 ASP 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 958 THR 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 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 209 THR 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 634 ILE 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 958 THR Chi-restraints excluded: chain E residue 980 THR 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 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: 6.9990 chunk 639 optimal weight: 2.9990 chunk 441 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 405 optimal weight: 7.9990 chunk 571 optimal weight: 3.9990 chunk 853 optimal weight: 4.9990 chunk 903 optimal weight: 4.9990 chunk 446 optimal weight: 4.9990 chunk 809 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 329 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A 976 ASN A1433 GLN ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN ** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1684 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 504 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN ** B1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1433 GLN ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1575 GLN ** B1770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1788 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN C 490 ASN C 504 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 ASN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1365 GLN C1408 GLN C1433 GLN ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1575 GLN ** C1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1788 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 ASN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 ASN ** D 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 844 ASN D1433 GLN ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1575 GLN ** D1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1770 ASN D1788 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN E 286 GLN ** E 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 490 ASN ** E 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 504 ASN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 646 ASN ** E 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1433 GLN E1575 GLN ** E1770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1788 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 76915 Z= 0.379 Angle : 0.683 10.626 104180 Z= 0.348 Chirality : 0.045 0.255 11525 Planarity : 0.005 0.071 13555 Dihedral : 5.567 27.018 10099 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.66 % Favored : 90.30 % Rotamer: Outliers : 3.53 % Allowed : 11.90 % Favored : 84.57 % 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: -1.21 (0.09), residues: 9345 helix: 0.63 (0.07), residues: 5115 sheet: -1.71 (0.21), residues: 560 loop : -2.81 (0.09), residues: 3670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 505 HIS 0.011 0.002 HIS C1095 PHE 0.025 0.002 PHE E1083 TYR 0.023 0.002 TYR A1820 ARG 0.009 0.001 ARG C1706 *********************** 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 1053 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 761 time to evaluate : 6.637 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: A 231 SER cc_start: 0.7706 (OUTLIER) cc_final: 0.7167 (t) REVERT: A 300 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7671 (m-40) REVERT: A 588 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8993 (mp) REVERT: A 671 MET cc_start: 0.5704 (mtp) cc_final: 0.5247 (mmm) REVERT: A 1626 SER cc_start: 0.9106 (t) cc_final: 0.8817 (p) REVERT: A 2012 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8409 (tp) REVERT: B 231 SER cc_start: 0.7628 (OUTLIER) cc_final: 0.7121 (t) REVERT: B 300 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7560 (m110) REVERT: B 1593 ILE cc_start: 0.8926 (pt) cc_final: 0.8407 (mt) REVERT: B 2012 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8184 (tp) REVERT: C 231 SER cc_start: 0.7608 (OUTLIER) cc_final: 0.7143 (t) REVERT: C 392 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8354 (p) REVERT: C 648 MET cc_start: 0.8007 (tmm) cc_final: 0.7688 (tmm) REVERT: C 1626 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8771 (p) REVERT: C 1793 MET cc_start: 0.8094 (mtm) cc_final: 0.7880 (ttm) REVERT: C 2012 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8292 (tp) REVERT: D 231 SER cc_start: 0.7887 (OUTLIER) cc_final: 0.7390 (t) REVERT: D 254 TRP cc_start: 0.7634 (t-100) cc_final: 0.7380 (t-100) REVERT: D 300 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7575 (m110) REVERT: D 414 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: D 588 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.9008 (mp) REVERT: D 613 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: D 696 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7266 (mp0) REVERT: D 1527 MET cc_start: 0.7226 (mtm) cc_final: 0.6987 (mtm) REVERT: D 1626 SER cc_start: 0.9090 (t) cc_final: 0.8763 (p) REVERT: D 2012 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8531 (tp) REVERT: E 231 SER cc_start: 0.7633 (OUTLIER) cc_final: 0.7070 (t) REVERT: E 300 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7687 (m110) REVERT: E 822 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7907 (pm20) REVERT: E 954 TYR cc_start: 0.8037 (m-10) cc_final: 0.7734 (m-80) REVERT: E 2012 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8243 (tp) outliers start: 292 outliers final: 182 residues processed: 991 average time/residue: 0.6756 time to fit residues: 1169.2543 Evaluate side-chains 867 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 665 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 170 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 VAL 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 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 745 ILE 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 980 THR Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1408 GLN Chi-restraints excluded: chain A residue 1477 ASP Chi-restraints excluded: chain A residue 1481 ILE Chi-restraints excluded: chain A residue 1519 ASN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1572 LEU Chi-restraints excluded: chain A residue 1575 GLN Chi-restraints excluded: chain A residue 1579 GLN Chi-restraints excluded: chain A residue 1615 LYS 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 1919 MET 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 170 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 VAL 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 389 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 772 MET 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 980 THR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1076 ASP Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1416 LEU Chi-restraints excluded: chain B residue 1477 ASP Chi-restraints excluded: chain B residue 1481 ILE Chi-restraints excluded: chain B residue 1519 ASN Chi-restraints excluded: chain B residue 1575 GLN 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 C residue 170 SER Chi-restraints excluded: chain C residue 203 GLU 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 375 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1269 LEU Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1408 GLN Chi-restraints excluded: chain C residue 1481 ILE Chi-restraints excluded: chain C residue 1519 ASN Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1575 GLN Chi-restraints excluded: chain C residue 1626 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 1904 LEU Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2027 THR Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 170 SER 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 389 VAL Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 613 GLN Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 729 ASP 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 955 ILE Chi-restraints excluded: chain D residue 958 THR Chi-restraints excluded: chain D residue 977 SER Chi-restraints excluded: chain D residue 980 THR 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 1477 ASP Chi-restraints excluded: chain D residue 1481 ILE Chi-restraints excluded: chain D residue 1519 ASN 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 1614 SER Chi-restraints excluded: chain D residue 1739 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 112 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 213 VAL 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 435 SER Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 634 ILE 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 955 ILE Chi-restraints excluded: chain E residue 958 THR Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 980 THR 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 1481 ILE Chi-restraints excluded: chain E residue 1519 ASN Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1575 GLN Chi-restraints excluded: chain E residue 1578 GLN Chi-restraints excluded: chain E residue 1615 LYS Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1644 ILE Chi-restraints excluded: chain E residue 1739 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 752 optimal weight: 0.5980 chunk 513 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 672 optimal weight: 1.9990 chunk 372 optimal weight: 0.0870 chunk 771 optimal weight: 0.9980 chunk 624 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 461 optimal weight: 4.9990 chunk 811 optimal weight: 6.9990 chunk 228 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 329 ASN A 493 HIS A 539 GLN A 563 GLN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1388 GLN ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN A1577 GLN ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1858 GLN B 90 GLN B 432 GLN B 490 ASN B 533 HIS ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1388 GLN ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1515 HIS C 90 GLN C 286 GLN C 490 ASN C 563 GLN ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN C1388 GLN ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1577 GLN ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1858 GLN ** C1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN D 490 ASN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 844 ASN D 976 ASN D1388 GLN ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1575 GLN E 90 GLN E 490 ASN E 493 HIS ** E 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1388 GLN ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1515 HIS ** E1770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 76915 Z= 0.149 Angle : 0.555 11.561 104180 Z= 0.282 Chirality : 0.039 0.257 11525 Planarity : 0.004 0.051 13555 Dihedral : 4.979 26.330 10095 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.27 % Allowed : 13.56 % Favored : 84.17 % 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: -0.64 (0.09), residues: 9345 helix: 1.22 (0.08), residues: 5080 sheet: -1.41 (0.22), residues: 540 loop : -2.73 (0.09), residues: 3725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 336 HIS 0.008 0.001 HIS A1095 PHE 0.016 0.001 PHE D 391 TYR 0.014 0.001 TYR B1484 ARG 0.009 0.000 ARG B1628 *********************** 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 963 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 775 time to evaluate : 6.985 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: 0.7601 (OUTLIER) cc_final: 0.7214 (t) REVERT: A 1626 SER cc_start: 0.8971 (t) cc_final: 0.8757 (p) REVERT: A 1941 TYR cc_start: 0.6709 (m-80) cc_final: 0.6403 (m-80) REVERT: A 2012 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8437 (tp) REVERT: B 231 SER cc_start: 0.7577 (OUTLIER) cc_final: 0.7143 (t) REVERT: B 300 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7568 (m-40) REVERT: B 677 LEU cc_start: 0.8126 (mt) cc_final: 0.7886 (mp) REVERT: B 738 ILE cc_start: 0.8650 (mt) cc_final: 0.8423 (mt) REVERT: B 1027 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8157 (tp-100) REVERT: B 2012 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8193 (tp) REVERT: C 231 SER cc_start: 0.7653 (OUTLIER) cc_final: 0.7238 (t) REVERT: C 648 MET cc_start: 0.7972 (tmm) cc_final: 0.7444 (tmm) REVERT: C 1626 SER cc_start: 0.8919 (t) cc_final: 0.8688 (p) REVERT: C 1878 MET cc_start: 0.5823 (mmp) cc_final: 0.5492 (mmm) REVERT: C 2012 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8277 (tp) REVERT: D 203 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6519 (tp30) REVERT: D 231 SER cc_start: 0.7740 (OUTLIER) cc_final: 0.7311 (t) REVERT: D 300 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7511 (m110) REVERT: D 414 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: D 432 GLN cc_start: 0.8373 (tp40) cc_final: 0.8094 (pt0) REVERT: D 696 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7242 (mp0) REVERT: D 738 ILE cc_start: 0.8549 (mt) cc_final: 0.8334 (mt) REVERT: D 1626 SER cc_start: 0.8947 (t) cc_final: 0.8703 (p) REVERT: D 1878 MET cc_start: 0.6071 (mmp) cc_final: 0.5701 (mmm) REVERT: D 2012 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8499 (tp) REVERT: E 231 SER cc_start: 0.7710 (OUTLIER) cc_final: 0.7266 (t) REVERT: E 648 MET cc_start: 0.7718 (tmm) cc_final: 0.7257 (tmm) REVERT: E 677 LEU cc_start: 0.8072 (mt) cc_final: 0.7844 (mp) REVERT: E 738 ILE cc_start: 0.8717 (mt) cc_final: 0.8470 (mt) REVERT: E 822 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7865 (pm20) REVERT: E 918 ILE cc_start: 0.8390 (mm) cc_final: 0.8126 (mm) REVERT: E 1471 ILE cc_start: 0.8438 (mm) cc_final: 0.8189 (mp) REVERT: E 1628 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7026 (mtm180) REVERT: E 1878 MET cc_start: 0.6024 (mmp) cc_final: 0.5644 (mmm) REVERT: E 2012 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8252 (tp) outliers start: 188 outliers final: 111 residues processed: 917 average time/residue: 0.6806 time to fit residues: 1091.6466 Evaluate side-chains 788 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 662 time to evaluate : 6.451 ------------------------------------------------------------------------------- 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 435 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1092 SER 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 1807 THR Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1919 MET 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 300 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1027 GLN Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1294 LEU 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 1768 LEU Chi-restraints excluded: chain B residue 1807 THR Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 203 GLU 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 389 VAL Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 483 ASN 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 787 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1076 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 1707 GLU Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1807 THR Chi-restraints excluded: chain C residue 1808 ASP Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain D residue 203 GLU 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 389 VAL Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 435 SER 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 958 THR Chi-restraints excluded: chain D residue 980 THR 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 1575 GLN Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1807 THR Chi-restraints excluded: chain D residue 1808 ASP Chi-restraints excluded: chain D residue 2012 LEU Chi-restraints excluded: chain E residue 61 ILE 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 414 GLN Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 958 THR Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1092 SER Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1739 GLN Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1807 THR Chi-restraints excluded: chain E residue 1808 ASP 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: 4.9990 chunk 813 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 530 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 904 optimal weight: 5.9990 chunk 750 optimal weight: 8.9990 chunk 418 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 299 optimal weight: 0.6980 chunk 474 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 GLN ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN ** A1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 ASN A1788 GLN A2005 ASN ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 HIS ** B1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1770 ASN B2005 ASN C 329 ASN C 490 ASN C 623 GLN C 976 ASN C1330 GLN ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1575 GLN ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1770 ASN C1845 GLN ** C1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2005 ASN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS D 623 GLN D 976 ASN ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1575 GLN ** E1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1770 ASN E2005 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 76915 Z= 0.377 Angle : 0.671 11.141 104180 Z= 0.340 Chirality : 0.044 0.267 11525 Planarity : 0.005 0.077 13555 Dihedral : 5.359 26.692 10095 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.62 % Favored : 90.34 % Rotamer: Outliers : 3.36 % Allowed : 13.20 % Favored : 83.44 % 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: -0.74 (0.09), residues: 9345 helix: 1.07 (0.08), residues: 5105 sheet: -1.35 (0.21), residues: 565 loop : -2.73 (0.10), residues: 3675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1077 HIS 0.008 0.001 HIS D1751 PHE 0.017 0.002 PHE C 492 TYR 0.022 0.002 TYR A1820 ARG 0.007 0.001 ARG A 635 *********************** 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 971 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 693 time to evaluate : 6.566 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: 0.7648 (OUTLIER) cc_final: 0.7126 (t) REVERT: A 559 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6636 (pp20) REVERT: A 671 MET cc_start: 0.5763 (OUTLIER) cc_final: 0.5268 (mmm) REVERT: A 2012 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8426 (tp) REVERT: B 231 SER cc_start: 0.7653 (OUTLIER) cc_final: 0.7119 (t) REVERT: B 254 TRP cc_start: 0.7543 (t-100) cc_final: 0.7332 (t-100) REVERT: B 300 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7480 (m-40) REVERT: B 954 TYR cc_start: 0.7987 (m-10) cc_final: 0.7768 (m-80) REVERT: B 1593 ILE cc_start: 0.8944 (pt) cc_final: 0.8381 (mt) REVERT: B 1878 MET cc_start: 0.6175 (mmp) cc_final: 0.5913 (mmm) REVERT: B 2012 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8149 (tp) REVERT: C 231 SER cc_start: 0.7656 (OUTLIER) cc_final: 0.7181 (t) REVERT: C 254 TRP cc_start: 0.7601 (t-100) cc_final: 0.7267 (t-100) REVERT: C 648 MET cc_start: 0.7989 (tmm) cc_final: 0.7683 (tmm) REVERT: C 954 TYR cc_start: 0.8180 (m-10) cc_final: 0.7798 (m-80) REVERT: C 1626 SER cc_start: 0.9107 (t) cc_final: 0.8770 (p) REVERT: C 2012 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8289 (tp) REVERT: D 231 SER cc_start: 0.7796 (OUTLIER) cc_final: 0.7301 (t) REVERT: D 300 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7455 (m110) REVERT: D 414 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: D 613 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: D 696 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7187 (mp0) REVERT: D 1626 SER cc_start: 0.9101 (t) cc_final: 0.8759 (p) REVERT: D 2012 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8512 (tp) REVERT: E 231 SER cc_start: 0.7779 (OUTLIER) cc_final: 0.7215 (t) REVERT: E 822 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7899 (pm20) REVERT: E 1471 ILE cc_start: 0.8567 (mm) cc_final: 0.8264 (mp) REVERT: E 1578 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: E 1593 ILE cc_start: 0.8962 (pt) cc_final: 0.8386 (mt) REVERT: E 2012 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8275 (tp) outliers start: 278 outliers final: 200 residues processed: 902 average time/residue: 0.6616 time to fit residues: 1050.1620 Evaluate side-chains 856 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 639 time to evaluate : 6.538 ------------------------------------------------------------------------------- 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 223 SER 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 435 SER Chi-restraints excluded: chain A residue 559 GLU 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 700 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 787 LEU 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 955 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1092 SER 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 1481 ILE Chi-restraints excluded: chain A residue 1519 ASN 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 1575 GLN Chi-restraints excluded: chain A residue 1579 GLN 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 1807 THR Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1919 MET Chi-restraints excluded: chain A residue 1937 LEU 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 76 ILE Chi-restraints excluded: chain B residue 112 ASP 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 389 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 772 MET Chi-restraints excluded: chain B residue 787 LEU 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 977 SER Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1027 GLN Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1076 ASP Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1133 PHE Chi-restraints excluded: chain B residue 1294 LEU 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 1807 THR Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1886 THR Chi-restraints excluded: chain B residue 1937 LEU 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 112 ASP Chi-restraints excluded: chain C residue 203 GLU 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 389 VAL Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 483 ASN 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 840 LEU Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 980 THR 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 1133 PHE Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1477 ASP Chi-restraints excluded: chain C residue 1519 ASN Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1570 MET Chi-restraints excluded: chain C residue 1614 SER Chi-restraints excluded: chain C residue 1642 VAL Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1807 THR Chi-restraints excluded: chain C residue 1808 ASP Chi-restraints excluded: chain C residue 1886 THR Chi-restraints excluded: chain C residue 1904 LEU Chi-restraints excluded: chain C residue 1937 LEU Chi-restraints excluded: chain C residue 1941 TYR 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 379 ARG Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 613 GLN Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 729 ASP 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 958 THR Chi-restraints excluded: chain D residue 977 SER Chi-restraints excluded: chain D residue 980 THR 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 1408 GLN Chi-restraints excluded: chain D residue 1481 ILE Chi-restraints excluded: chain D residue 1519 ASN Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1627 SER Chi-restraints excluded: chain D residue 1739 GLN Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1802 VAL Chi-restraints excluded: chain D residue 1807 THR 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 203 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 223 SER 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 435 SER Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 713 ASN Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 886 VAL Chi-restraints excluded: chain E residue 955 ILE Chi-restraints excluded: chain E residue 958 THR Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 980 THR Chi-restraints excluded: chain E residue 1027 GLN Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1076 ASP Chi-restraints excluded: chain E residue 1086 ASP Chi-restraints excluded: chain E residue 1092 SER Chi-restraints excluded: chain E residue 1103 ASP Chi-restraints excluded: chain E residue 1133 PHE Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1473 LEU Chi-restraints excluded: chain E residue 1519 ASN Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1578 GLN Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1739 GLN Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1807 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 872 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 515 optimal weight: 2.9990 chunk 660 optimal weight: 0.8980 chunk 511 optimal weight: 0.9980 chunk 761 optimal weight: 0.8980 chunk 505 optimal weight: 0.1980 chunk 901 optimal weight: 4.9990 chunk 563 optimal weight: 2.9990 chunk 549 optimal weight: 6.9990 chunk 416 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1515 HIS A1575 GLN ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2005 ASN B 437 GLN B 490 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN ** B1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2005 ASN C 437 GLN C 490 ASN ** C 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1575 GLN ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2005 ASN D 437 GLN D 976 ASN ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1515 HIS ** D1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN E 437 GLN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 976 ASN ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2005 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 76915 Z= 0.161 Angle : 0.565 11.544 104180 Z= 0.284 Chirality : 0.039 0.248 11525 Planarity : 0.004 0.049 13555 Dihedral : 4.948 26.420 10095 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.50 % Allowed : 14.61 % Favored : 82.89 % 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: -0.34 (0.09), residues: 9345 helix: 1.51 (0.08), residues: 5050 sheet: -1.11 (0.23), residues: 540 loop : -2.68 (0.09), residues: 3755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 336 HIS 0.008 0.001 HIS E1095 PHE 0.021 0.001 PHE A 747 TYR 0.015 0.001 TYR C1484 ARG 0.009 0.000 ARG C 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 907 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 700 time to evaluate : 6.643 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: A 231 SER cc_start: 0.7566 (OUTLIER) cc_final: 0.7155 (t) REVERT: A 671 MET cc_start: 0.5585 (OUTLIER) cc_final: 0.5112 (mmm) REVERT: A 1626 SER cc_start: 0.9005 (t) cc_final: 0.8771 (p) REVERT: A 1941 TYR cc_start: 0.6640 (m-80) cc_final: 0.6363 (m-80) REVERT: A 2012 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8419 (tp) REVERT: B 231 SER cc_start: 0.7562 (OUTLIER) cc_final: 0.7129 (t) REVERT: B 300 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7449 (m-40) REVERT: B 677 LEU cc_start: 0.8104 (mt) cc_final: 0.7876 (mp) REVERT: B 738 ILE cc_start: 0.8650 (mt) cc_final: 0.8394 (mt) REVERT: B 954 TYR cc_start: 0.8011 (m-10) cc_final: 0.7802 (m-80) REVERT: B 1110 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7943 (m110) REVERT: B 1297 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8626 (t80) REVERT: B 2012 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8206 (tp) REVERT: C 231 SER cc_start: 0.7605 (OUTLIER) cc_final: 0.7188 (t) REVERT: C 254 TRP cc_start: 0.7562 (t-100) cc_final: 0.7271 (t-100) REVERT: C 648 MET cc_start: 0.7942 (tmm) cc_final: 0.7552 (tmm) REVERT: C 708 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7313 (mp10) REVERT: C 954 TYR cc_start: 0.8150 (m-10) cc_final: 0.7778 (m-80) REVERT: C 1297 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8373 (t80) REVERT: C 1626 SER cc_start: 0.8939 (t) cc_final: 0.8641 (p) REVERT: C 1878 MET cc_start: 0.5889 (mmp) cc_final: 0.5552 (mmm) REVERT: C 2012 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8284 (tp) REVERT: D 203 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6663 (tp30) REVERT: D 231 SER cc_start: 0.7736 (OUTLIER) cc_final: 0.7296 (t) REVERT: D 254 TRP cc_start: 0.7552 (t-100) cc_final: 0.7277 (t-100) REVERT: D 300 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7365 (m-40) REVERT: D 401 TYR cc_start: 0.7398 (m-80) cc_final: 0.7186 (m-80) REVERT: D 414 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: D 432 GLN cc_start: 0.8379 (tp40) cc_final: 0.8097 (pt0) REVERT: D 692 LYS cc_start: 0.7117 (mttt) cc_final: 0.6447 (ttmt) REVERT: D 696 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7239 (mp0) REVERT: D 738 ILE cc_start: 0.8579 (mt) cc_final: 0.8372 (mt) REVERT: D 1297 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8884 (t80) REVERT: D 1626 SER cc_start: 0.8996 (t) cc_final: 0.8719 (p) REVERT: D 1878 MET cc_start: 0.6117 (mmp) cc_final: 0.5734 (mmm) REVERT: D 2012 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8502 (tp) REVERT: E 231 SER cc_start: 0.7680 (OUTLIER) cc_final: 0.7224 (t) REVERT: E 380 MET cc_start: 0.8349 (mtp) cc_final: 0.8148 (mtp) REVERT: E 648 MET cc_start: 0.7739 (tmm) cc_final: 0.7291 (tmm) REVERT: E 738 ILE cc_start: 0.8698 (mt) cc_final: 0.8460 (mt) REVERT: E 822 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7862 (pm20) REVERT: E 1297 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8614 (t80) REVERT: E 1471 ILE cc_start: 0.8520 (mm) cc_final: 0.8273 (mp) REVERT: E 1527 MET cc_start: 0.7002 (mtm) cc_final: 0.6477 (mtm) REVERT: E 1849 GLU cc_start: 0.7027 (mp0) cc_final: 0.6818 (mp0) REVERT: E 2012 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8261 (tp) outliers start: 207 outliers final: 146 residues processed: 854 average time/residue: 0.6755 time to fit residues: 1014.2196 Evaluate side-chains 811 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 644 time to evaluate : 7.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLU 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 346 ILE 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 435 SER Chi-restraints excluded: chain A residue 596 LEU 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 713 ASN Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1027 GLN 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 1575 GLN 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 1807 THR Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1919 MET Chi-restraints excluded: chain A residue 1937 LEU 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 346 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1297 PHE Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1416 LEU Chi-restraints excluded: chain B residue 1519 ASN 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 1807 THR 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 346 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 708 GLN 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 955 ILE Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1269 LEU Chi-restraints excluded: chain C residue 1297 PHE 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 1575 GLN Chi-restraints excluded: chain C residue 1579 GLN Chi-restraints excluded: chain C residue 1642 VAL Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1807 THR 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 D residue 76 ILE Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 223 SER 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 379 ARG Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 435 SER 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 955 ILE Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1294 LEU Chi-restraints excluded: chain D residue 1297 PHE 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 1579 GLN Chi-restraints excluded: chain D residue 1739 GLN Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1807 THR 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 203 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 223 SER 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 414 GLN Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 958 THR Chi-restraints excluded: chain E residue 980 THR Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1103 ASP Chi-restraints excluded: chain E residue 1297 PHE Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1739 GLN Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1807 THR Chi-restraints excluded: chain E residue 1808 ASP Chi-restraints excluded: chain E residue 1949 ASP 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: 7.9990 chunk 359 optimal weight: 0.9990 chunk 538 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 572 optimal weight: 5.9990 chunk 613 optimal weight: 0.0870 chunk 445 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 708 optimal weight: 5.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- 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 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN ** A1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 437 GLN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1577 GLN B1684 GLN C 437 GLN C 802 HIS ** C 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1575 GLN ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 802 HIS E 976 ASN ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4479 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= 0.206 Angle : 0.576 11.193 104180 Z= 0.290 Chirality : 0.040 0.275 11525 Planarity : 0.004 0.048 13555 Dihedral : 4.884 25.996 10095 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.76 % Allowed : 14.43 % Favored : 82.82 % 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: -0.20 (0.09), residues: 9345 helix: 1.61 (0.08), residues: 5045 sheet: -1.05 (0.23), residues: 555 loop : -2.60 (0.10), residues: 3745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1077 HIS 0.006 0.001 HIS E1095 PHE 0.017 0.001 PHE C1574 TYR 0.017 0.001 TYR B1468 ARG 0.009 0.000 ARG D 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 905 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 677 time to evaluate : 6.696 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: 0.7610 (OUTLIER) cc_final: 0.7179 (t) REVERT: A 559 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: A 671 MET cc_start: 0.5687 (OUTLIER) cc_final: 0.5189 (mmm) REVERT: A 708 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7090 (mp10) REVERT: A 1411 GLN cc_start: 0.8226 (tp40) cc_final: 0.7986 (tp40) REVERT: A 1626 SER cc_start: 0.9065 (t) cc_final: 0.8755 (p) REVERT: A 2012 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8403 (tp) REVERT: B 231 SER cc_start: 0.7617 (OUTLIER) cc_final: 0.7166 (t) REVERT: B 300 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7443 (m-40) REVERT: B 677 LEU cc_start: 0.8047 (mt) cc_final: 0.7817 (mp) REVERT: B 954 TYR cc_start: 0.8013 (m-10) cc_final: 0.7625 (m-80) REVERT: B 1110 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7968 (m110) REVERT: B 1297 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8759 (t80) REVERT: B 1878 MET cc_start: 0.6148 (mmp) cc_final: 0.5882 (mmm) REVERT: B 2012 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8210 (tp) REVERT: C 231 SER cc_start: 0.7639 (OUTLIER) cc_final: 0.7234 (t) REVERT: C 254 TRP cc_start: 0.7604 (t-100) cc_final: 0.7357 (t-100) REVERT: C 648 MET cc_start: 0.7947 (tmm) cc_final: 0.7637 (tmm) REVERT: C 954 TYR cc_start: 0.8183 (m-10) cc_final: 0.7832 (m-80) REVERT: C 1297 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8523 (t80) REVERT: C 1626 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8669 (p) REVERT: C 2012 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8271 (tp) REVERT: D 203 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6640 (tp30) REVERT: D 231 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7312 (t) REVERT: D 254 TRP cc_start: 0.7552 (t-100) cc_final: 0.7310 (t-100) REVERT: D 300 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7409 (m110) REVERT: D 414 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: D 1297 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8991 (t80) REVERT: D 1534 LEU cc_start: 0.8402 (pp) cc_final: 0.8115 (tt) REVERT: D 1626 SER cc_start: 0.9037 (t) cc_final: 0.8711 (p) REVERT: D 2012 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8493 (tp) REVERT: E 231 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7319 (t) REVERT: E 738 ILE cc_start: 0.8707 (mt) cc_final: 0.8487 (mt) REVERT: E 822 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7875 (pm20) REVERT: E 1291 LYS cc_start: 0.8670 (mttm) cc_final: 0.8459 (mtmm) REVERT: E 1297 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8702 (t80) REVERT: E 1471 ILE cc_start: 0.8519 (mm) cc_final: 0.8242 (mp) REVERT: E 1527 MET cc_start: 0.7088 (mtm) cc_final: 0.6651 (mtm) REVERT: E 1628 ARG cc_start: 0.7431 (mtt180) cc_final: 0.7056 (mtm180) REVERT: E 1849 GLU cc_start: 0.7029 (mp0) cc_final: 0.6807 (mp0) REVERT: E 2012 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8257 (tp) outliers start: 228 outliers final: 170 residues processed: 842 average time/residue: 0.7135 time to fit residues: 1064.4828 Evaluate side-chains 837 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 644 time to evaluate : 6.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 346 ILE 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 435 SER Chi-restraints excluded: chain A residue 559 GLU 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 707 ILE Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1027 GLN 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 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 1807 THR Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1937 LEU 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 76 ILE Chi-restraints excluded: chain B residue 112 ASP 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 389 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 435 SER 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 729 ASP Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1076 ASP Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1297 PHE Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1416 LEU Chi-restraints excluded: chain B residue 1519 ASN 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 1807 THR 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 231 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 522 ILE 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 860 VAL Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 980 THR 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 1297 PHE Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1519 ASN Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1575 GLN Chi-restraints excluded: chain C residue 1579 GLN Chi-restraints excluded: chain C residue 1626 SER Chi-restraints excluded: chain C residue 1642 VAL Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1807 THR 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 1941 TYR 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 78 GLU Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 223 SER 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 379 ARG Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 442 THR 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 832 LEU Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1294 LEU Chi-restraints excluded: chain D residue 1297 PHE Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1408 GLN Chi-restraints excluded: chain D residue 1473 LEU Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1579 GLN Chi-restraints excluded: chain D residue 1627 SER Chi-restraints excluded: chain D residue 1719 LYS Chi-restraints excluded: chain D residue 1739 GLN Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1807 THR 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 203 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 223 SER 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 414 GLN Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 713 ASN Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 958 THR Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 980 THR 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 1297 PHE Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1473 LEU Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1739 GLN Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1807 THR 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: 4.9990 chunk 863 optimal weight: 0.5980 chunk 787 optimal weight: 0.4980 chunk 839 optimal weight: 3.9990 chunk 505 optimal weight: 7.9990 chunk 365 optimal weight: 4.9990 chunk 659 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 chunk 758 optimal weight: 2.9990 chunk 794 optimal weight: 2.9990 chunk 836 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN ** A1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1330 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** C1575 GLN ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1575 GLN ** D1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 76915 Z= 0.256 Angle : 0.605 11.032 104180 Z= 0.305 Chirality : 0.041 0.272 11525 Planarity : 0.004 0.049 13555 Dihedral : 5.007 26.688 10095 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 2.76 % Allowed : 14.65 % Favored : 82.60 % 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: -0.22 (0.09), residues: 9345 helix: 1.57 (0.08), residues: 5055 sheet: -1.06 (0.22), residues: 555 loop : -2.57 (0.10), residues: 3735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 336 HIS 0.007 0.001 HIS E1095 PHE 0.018 0.002 PHE A 747 TYR 0.016 0.001 TYR A1820 ARG 0.008 0.001 ARG A 635 *********************** 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 894 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 666 time to evaluate : 6.709 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 191 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8007 (tt) REVERT: A 231 SER cc_start: 0.7572 (OUTLIER) cc_final: 0.7130 (t) REVERT: A 708 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: A 1291 LYS cc_start: 0.8708 (mttm) cc_final: 0.8457 (mtmm) REVERT: A 1411 GLN cc_start: 0.8324 (tp40) cc_final: 0.8038 (tp40) REVERT: A 1626 SER cc_start: 0.9095 (t) cc_final: 0.8779 (p) REVERT: A 2012 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8404 (tp) REVERT: B 231 SER cc_start: 0.7585 (OUTLIER) cc_final: 0.7125 (t) REVERT: B 300 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7449 (m-40) REVERT: B 708 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: B 934 TYR cc_start: 0.7104 (m-10) cc_final: 0.6851 (m-10) REVERT: B 948 MET cc_start: 0.8212 (mmm) cc_final: 0.7990 (mmm) REVERT: B 954 TYR cc_start: 0.8032 (m-10) cc_final: 0.7770 (m-80) REVERT: B 1110 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7967 (m110) REVERT: B 1275 LEU cc_start: 0.7890 (tp) cc_final: 0.7395 (mp) REVERT: B 1297 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8861 (t80) REVERT: B 1593 ILE cc_start: 0.8921 (pt) cc_final: 0.8343 (mt) REVERT: B 1878 MET cc_start: 0.6143 (mmp) cc_final: 0.5876 (mmm) REVERT: B 2012 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8185 (tp) REVERT: C 231 SER cc_start: 0.7655 (OUTLIER) cc_final: 0.7218 (t) REVERT: C 254 TRP cc_start: 0.7634 (t-100) cc_final: 0.7407 (t-100) REVERT: C 648 MET cc_start: 0.7940 (tmm) cc_final: 0.7635 (tmm) REVERT: C 708 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: C 954 TYR cc_start: 0.8221 (m-10) cc_final: 0.7860 (m-80) REVERT: C 1297 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8505 (t80) REVERT: C 1626 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8722 (p) REVERT: C 2012 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8285 (tp) REVERT: D 191 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7993 (tt) REVERT: D 203 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6689 (tp30) REVERT: D 231 SER cc_start: 0.7759 (OUTLIER) cc_final: 0.7274 (t) REVERT: D 254 TRP cc_start: 0.7560 (t-100) cc_final: 0.7335 (t-100) REVERT: D 300 ASN cc_start: 0.7839 (OUTLIER) cc_final: 0.7425 (m110) REVERT: D 414 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: D 696 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7232 (mp0) REVERT: D 918 ILE cc_start: 0.8134 (mt) cc_final: 0.7765 (tp) REVERT: D 1275 LEU cc_start: 0.7925 (tp) cc_final: 0.7382 (mp) REVERT: D 1297 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8990 (t80) REVERT: D 1626 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8718 (p) REVERT: D 1878 MET cc_start: 0.6149 (mmp) cc_final: 0.5753 (mmm) REVERT: D 2012 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8492 (tp) REVERT: E 191 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8093 (tt) REVERT: E 231 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7314 (t) REVERT: E 738 ILE cc_start: 0.8743 (mt) cc_final: 0.8526 (mt) REVERT: E 822 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7872 (pm20) REVERT: E 918 ILE cc_start: 0.8546 (mm) cc_final: 0.7820 (tp) REVERT: E 1291 LYS cc_start: 0.8717 (mttm) cc_final: 0.8488 (mtmm) REVERT: E 1297 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8750 (t80) REVERT: E 1471 ILE cc_start: 0.8512 (mm) cc_final: 0.8250 (mp) REVERT: E 1527 MET cc_start: 0.7116 (mtm) cc_final: 0.6760 (mtm) REVERT: E 1628 ARG cc_start: 0.7444 (mtt180) cc_final: 0.7070 (mtm180) REVERT: E 1849 GLU cc_start: 0.7066 (mp0) cc_final: 0.6814 (mp0) REVERT: E 2012 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8274 (tp) outliers start: 228 outliers final: 190 residues processed: 841 average time/residue: 0.6599 time to fit residues: 983.2210 Evaluate side-chains 862 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 645 time to evaluate : 6.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 346 ILE 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 435 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 787 LEU 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 980 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1092 SER 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 1519 ASN Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1575 GLN Chi-restraints excluded: chain A residue 1579 GLN 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 1807 THR Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1937 LEU 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 76 ILE Chi-restraints excluded: chain B residue 112 ASP 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 389 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 435 SER 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 729 ASP Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1076 ASP Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1294 LEU Chi-restraints excluded: chain B residue 1297 PHE Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1416 LEU Chi-restraints excluded: chain B residue 1519 ASN 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 1807 THR 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 191 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 346 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 708 GLN 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 860 VAL Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 977 SER Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1092 SER Chi-restraints excluded: chain C residue 1103 ASP Chi-restraints excluded: chain C residue 1133 PHE Chi-restraints excluded: chain C residue 1269 LEU Chi-restraints excluded: chain C residue 1297 PHE Chi-restraints excluded: chain C residue 1404 LEU Chi-restraints excluded: chain C residue 1519 ASN Chi-restraints excluded: chain C residue 1539 LEU Chi-restraints excluded: chain C residue 1570 MET Chi-restraints excluded: chain C residue 1575 GLN Chi-restraints excluded: chain C residue 1579 GLN Chi-restraints excluded: chain C residue 1626 SER Chi-restraints excluded: chain C residue 1642 VAL Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1739 GLN Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1807 THR Chi-restraints excluded: chain C residue 1808 ASP Chi-restraints excluded: chain C residue 1886 THR Chi-restraints excluded: chain C residue 1904 LEU 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 191 ILE Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 223 SER 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 379 ARG Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 745 ILE 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 980 THR 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 1297 PHE Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1408 GLN Chi-restraints excluded: chain D residue 1519 ASN 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 1626 SER Chi-restraints excluded: chain D residue 1627 SER Chi-restraints excluded: chain D residue 1644 ILE Chi-restraints excluded: chain D residue 1719 LYS Chi-restraints excluded: chain D residue 1739 GLN Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1807 THR 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 1944 VAL 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 112 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 223 SER 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 414 GLN Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 483 ASN Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 713 ASN Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 958 THR Chi-restraints excluded: chain E residue 977 SER Chi-restraints excluded: chain E residue 980 THR 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 1297 PHE Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1445 HIS Chi-restraints excluded: chain E residue 1473 LEU Chi-restraints excluded: chain E residue 1519 ASN Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1739 GLN Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1807 THR Chi-restraints excluded: chain E residue 1808 ASP Chi-restraints excluded: chain E residue 1886 THR Chi-restraints excluded: chain E residue 1949 ASP 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: 7.9990 chunk 888 optimal weight: 0.8980 chunk 542 optimal weight: 4.9990 chunk 421 optimal weight: 0.0570 chunk 617 optimal weight: 1.9990 chunk 931 optimal weight: 0.5980 chunk 857 optimal weight: 2.9990 chunk 741 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 572 optimal weight: 4.9990 chunk 454 optimal weight: 0.0020 overall best weight: 0.7108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN ** C 762 HIS ** 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 C1575 GLN ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1858 GLN E 437 GLN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 976 ASN ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 76915 Z= 0.155 Angle : 0.555 11.561 104180 Z= 0.279 Chirality : 0.039 0.263 11525 Planarity : 0.004 0.047 13555 Dihedral : 4.743 26.250 10095 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 2.18 % Allowed : 15.30 % Favored : 82.53 % 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: 0.02 (0.09), residues: 9345 helix: 1.79 (0.08), residues: 5055 sheet: -0.94 (0.23), residues: 540 loop : -2.50 (0.10), residues: 3750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 336 HIS 0.007 0.001 HIS E1095 PHE 0.028 0.001 PHE A1574 TYR 0.016 0.001 TYR D1484 ARG 0.009 0.000 ARG D 635 ********************** 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 885 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 705 time to evaluate : 6.543 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: 0.7559 (OUTLIER) cc_final: 0.7163 (t) REVERT: A 708 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: A 918 ILE cc_start: 0.8425 (mm) cc_final: 0.8192 (tp) REVERT: A 1291 LYS cc_start: 0.8642 (mttm) cc_final: 0.8415 (mtmm) REVERT: A 1411 GLN cc_start: 0.8276 (tp40) cc_final: 0.7969 (tp40) REVERT: A 1626 SER cc_start: 0.8986 (t) cc_final: 0.8726 (p) REVERT: A 2012 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8393 (tp) REVERT: B 231 SER cc_start: 0.7559 (OUTLIER) cc_final: 0.7163 (t) REVERT: B 254 TRP cc_start: 0.7394 (t-100) cc_final: 0.7177 (t-100) REVERT: B 300 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7454 (m-40) REVERT: B 708 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: B 934 TYR cc_start: 0.7034 (m-10) cc_final: 0.6785 (m-10) REVERT: B 1110 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7957 (m110) REVERT: B 1291 LYS cc_start: 0.8636 (mttm) cc_final: 0.8412 (mtmm) REVERT: B 2012 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8210 (tp) REVERT: C 191 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8169 (tt) REVERT: C 231 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7246 (t) REVERT: C 254 TRP cc_start: 0.7618 (t-100) cc_final: 0.7394 (t-100) REVERT: C 648 MET cc_start: 0.7943 (tmm) cc_final: 0.7589 (tmm) REVERT: C 708 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7411 (mp10) REVERT: C 954 TYR cc_start: 0.8175 (m-10) cc_final: 0.7808 (m-80) REVERT: C 1291 LYS cc_start: 0.8650 (mttm) cc_final: 0.8440 (mtmm) REVERT: C 1297 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8352 (t80) REVERT: C 1575 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: C 1626 SER cc_start: 0.8932 (t) cc_final: 0.8644 (p) REVERT: C 2012 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8259 (tp) REVERT: D 203 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6639 (tp30) REVERT: D 231 SER cc_start: 0.7706 (OUTLIER) cc_final: 0.7263 (t) REVERT: D 300 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7391 (m110) REVERT: D 432 GLN cc_start: 0.8340 (tp40) cc_final: 0.8044 (pt0) REVERT: D 635 ARG cc_start: 0.7397 (mtm110) cc_final: 0.7011 (mtm110) REVERT: D 918 ILE cc_start: 0.8132 (mt) cc_final: 0.7760 (tp) REVERT: D 1291 LYS cc_start: 0.8531 (mttm) cc_final: 0.8321 (mtmm) REVERT: D 1626 SER cc_start: 0.8960 (t) cc_final: 0.8686 (p) REVERT: D 1739 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: D 1878 MET cc_start: 0.6156 (mmp) cc_final: 0.5808 (mmm) REVERT: D 2012 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8481 (tp) REVERT: E 191 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8191 (tt) REVERT: E 231 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7334 (t) REVERT: E 414 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7803 (mp10) REVERT: E 738 ILE cc_start: 0.8680 (mt) cc_final: 0.8426 (mt) REVERT: E 822 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7874 (pm20) REVERT: E 918 ILE cc_start: 0.8516 (mm) cc_final: 0.7797 (tp) REVERT: E 1291 LYS cc_start: 0.8636 (mttm) cc_final: 0.8425 (mtmm) REVERT: E 1471 ILE cc_start: 0.8499 (mm) cc_final: 0.8265 (mp) REVERT: E 1527 MET cc_start: 0.6979 (mtm) cc_final: 0.6701 (mtm) REVERT: E 1628 ARG cc_start: 0.7358 (mtt180) cc_final: 0.7039 (mtm180) REVERT: E 1849 GLU cc_start: 0.7044 (mp0) cc_final: 0.6771 (mp0) REVERT: E 2012 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8247 (tp) outliers start: 180 outliers final: 145 residues processed: 837 average time/residue: 0.6787 time to fit residues: 1001.5992 Evaluate side-chains 826 residues out of total 8285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 658 time to evaluate : 6.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 203 GLU 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 346 ILE Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 980 THR 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 1575 GLN Chi-restraints excluded: chain A residue 1579 GLN 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 1807 THR Chi-restraints excluded: chain A residue 1808 ASP Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1937 LEU 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 346 ILE Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 522 ILE 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 729 ASP Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain B residue 1103 ASP Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1294 LEU 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 1807 THR 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 191 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 346 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 634 ILE Chi-restraints excluded: chain C residue 708 GLN 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 958 THR Chi-restraints excluded: chain C residue 977 SER 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 1297 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 1579 GLN Chi-restraints excluded: chain C residue 1642 VAL Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1768 LEU Chi-restraints excluded: chain C residue 1807 THR 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 D residue 76 ILE Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 223 SER 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 379 ARG Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 832 LEU 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 1627 SER Chi-restraints excluded: chain D residue 1644 ILE Chi-restraints excluded: chain D residue 1739 GLN Chi-restraints excluded: chain D residue 1768 LEU Chi-restraints excluded: chain D residue 1807 THR 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 191 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 223 SER 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 414 GLN Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 713 ASN Chi-restraints excluded: chain E residue 745 ILE Chi-restraints excluded: chain E residue 832 LEU Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 958 THR Chi-restraints excluded: chain E residue 1064 ILE Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1445 HIS Chi-restraints excluded: chain E residue 1519 ASN Chi-restraints excluded: chain E residue 1539 LEU Chi-restraints excluded: chain E residue 1642 VAL Chi-restraints excluded: chain E residue 1739 GLN Chi-restraints excluded: chain E residue 1768 LEU Chi-restraints excluded: chain E residue 1807 THR Chi-restraints excluded: chain E residue 1808 ASP Chi-restraints excluded: chain E residue 1886 THR Chi-restraints excluded: chain E residue 1949 ASP 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: 1.9990 chunk 790 optimal weight: 0.0070 chunk 227 optimal weight: 0.1980 chunk 683 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 742 optimal weight: 8.9990 chunk 310 optimal weight: 1.9990 chunk 762 optimal weight: 0.0570 chunk 94 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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** A 509 ASN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN ** A1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN B 509 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN C 509 ASN ** C 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1575 GLN C1684 GLN ** C1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN ** D 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN E 509 ASN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 989 GLN ** E1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.132766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104379 restraints weight = 131981.609| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.54 r_work: 0.3214 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 76915 Z= 0.151 Angle : 0.554 12.052 104180 Z= 0.279 Chirality : 0.039 0.257 11525 Planarity : 0.004 0.048 13555 Dihedral : 4.632 25.955 10095 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 2.07 % Allowed : 15.41 % Favored : 82.53 % 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: 0.15 (0.09), residues: 9345 helix: 1.90 (0.08), residues: 5055 sheet: -0.92 (0.23), residues: 540 loop : -2.44 (0.10), residues: 3750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 336 HIS 0.006 0.001 HIS E1095 PHE 0.020 0.001 PHE A1574 TYR 0.016 0.001 TYR E1468 ARG 0.010 0.000 ARG A 635 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20995.78 seconds wall clock time: 368 minutes 50.12 seconds (22130.12 seconds total)