Starting phenix.real_space_refine on Tue Apr 9 20:13:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjc_0011/04_2024/6gjc_0011_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjc_0011/04_2024/6gjc_0011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjc_0011/04_2024/6gjc_0011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjc_0011/04_2024/6gjc_0011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjc_0011/04_2024/6gjc_0011_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjc_0011/04_2024/6gjc_0011_updated.pdb" } resolution = 3.3 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 390 5.16 5 C 78570 2.51 5 N 22242 2.21 5 O 23784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 2806": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.28s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 124992 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 20801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2770, 20801 Classifications: {'peptide': 2770} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 152, 'TRANS': 2617} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 20801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2770, 20801 Classifications: {'peptide': 2770} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 152, 'TRANS': 2617} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 20801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2770, 20801 Classifications: {'peptide': 2770} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 152, 'TRANS': 2617} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 20801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2770, 20801 Classifications: {'peptide': 2770} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 152, 'TRANS': 2617} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 20801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2770, 20801 Classifications: {'peptide': 2770} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 152, 'TRANS': 2617} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 20801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2770, 20801 Classifications: {'peptide': 2770} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 152, 'TRANS': 2617} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 45.56, per 1000 atoms: 0.36 Number of scatterers: 124992 At special positions: 0 Unit cell: (228.718, 241.366, 274.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 390 16.00 P 6 15.00 O 23784 8.00 N 22242 7.00 C 78570 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: 36.31 Conformation dependent library (CDL) restraints added in 16.4 seconds 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 30216 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 714 helices and 138 sheets defined 52.5% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 36.56 Creating SS restraints... Processing helix chain 'A' and resid 32 through 41 Processing helix chain 'A' and resid 54 through 67 removed outlier: 4.325A pdb=" N THR A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 84 removed outlier: 3.574A pdb=" N ASP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 95 removed outlier: 4.611A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.553A pdb=" N TRP A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 122 through 144 Proline residue: A 127 - end of helix removed outlier: 3.854A pdb=" N LEU A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 161 through 171 removed outlier: 4.412A pdb=" N GLY A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 197 removed outlier: 3.871A pdb=" N ALA A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 removed outlier: 4.021A pdb=" N ASP A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 276 removed outlier: 4.096A pdb=" N LYS A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 316 removed outlier: 4.339A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 330 removed outlier: 4.796A pdb=" N ALA A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 366 - end of helix Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 399 through 405 removed outlier: 4.137A pdb=" N TYR A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 419 through 426 Processing helix chain 'A' and resid 441 through 452 removed outlier: 3.763A pdb=" N GLY A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 Processing helix chain 'A' and resid 493 through 501 Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 528 through 543 removed outlier: 3.647A pdb=" N ILE A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 568 removed outlier: 3.589A pdb=" N VAL A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) Proline residue: A 568 - end of helix Processing helix chain 'A' and resid 589 through 605 removed outlier: 5.828A pdb=" N SER A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 627 removed outlier: 4.003A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 634 removed outlier: 4.899A pdb=" N ALA A 632 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR A 633 " --> pdb=" O TRP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 651 removed outlier: 5.251A pdb=" N ALA A 649 " --> pdb=" O VAL A 645 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 645 through 651' Processing helix chain 'A' and resid 658 through 669 removed outlier: 5.784A pdb=" N GLN A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 713 removed outlier: 3.671A pdb=" N CYS A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 723 removed outlier: 3.554A pdb=" N ALA A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 734 removed outlier: 4.783A pdb=" N ALA A 734 " --> pdb=" O MET A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 745 removed outlier: 3.686A pdb=" N MET A 744 " --> pdb=" O ASP A 740 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 745' Processing helix chain 'A' and resid 746 through 758 Processing helix chain 'A' and resid 776 through 795 Processing helix chain 'A' and resid 809 through 815 Proline residue: A 815 - end of helix Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.798A pdb=" N ARG A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Proline residue: A 827 - end of helix Processing helix chain 'A' and resid 835 through 848 removed outlier: 4.077A pdb=" N VAL A 839 " --> pdb=" O HIS A 835 " (cutoff:3.500A) Proline residue: A 840 - end of helix removed outlier: 4.277A pdb=" N THR A 848 " --> pdb=" O THR A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 881 through 886 removed outlier: 4.077A pdb=" N VAL A 885 " --> pdb=" O ASP A 881 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS A 886 " --> pdb=" O ALA A 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 881 through 886' Processing helix chain 'A' and resid 890 through 898 removed outlier: 4.581A pdb=" N VAL A 894 " --> pdb=" O GLY A 890 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA A 895 " --> pdb=" O THR A 891 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THR A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 921 removed outlier: 4.093A pdb=" N ALA A 915 " --> pdb=" O PHE A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 949 removed outlier: 3.650A pdb=" N VAL A 945 " --> pdb=" O GLY A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 968 removed outlier: 4.030A pdb=" N ALA A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1023 removed outlier: 4.781A pdb=" N VAL A1021 " --> pdb=" O PRO A1017 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP A1022 " --> pdb=" O ALA A1018 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY A1023 " --> pdb=" O ASN A1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1017 through 1023' Processing helix chain 'A' and resid 1029 through 1046 Processing helix chain 'A' and resid 1068 through 1080 removed outlier: 4.211A pdb=" N VAL A1072 " --> pdb=" O HIS A1068 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A1073 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A1078 " --> pdb=" O ASP A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 4.755A pdb=" N VAL A1098 " --> pdb=" O PRO A1094 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLY A1099 " --> pdb=" O ASP A1095 " (cutoff:3.500A) Proline residue: A1100 - end of helix No H-bonds generated for 'chain 'A' and resid 1094 through 1102' Processing helix chain 'A' and resid 1103 through 1112 removed outlier: 3.535A pdb=" N SER A1111 " --> pdb=" O ALA A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1238 Processing helix chain 'A' and resid 1241 through 1246 removed outlier: 4.212A pdb=" N THR A1245 " --> pdb=" O ASN A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1254 Processing helix chain 'A' and resid 1261 through 1275 Processing helix chain 'A' and resid 1357 through 1364 Processing helix chain 'A' and resid 1365 through 1382 Processing helix chain 'A' and resid 1385 through 1392 Processing helix chain 'A' and resid 1413 through 1436 removed outlier: 4.153A pdb=" N GLY A1436 " --> pdb=" O MET A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1457 removed outlier: 5.458A pdb=" N TYR A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR A1453 " --> pdb=" O VAL A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1482 removed outlier: 4.023A pdb=" N ASP A1480 " --> pdb=" O SER A1476 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A1481 " --> pdb=" O LYS A1477 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL A1482 " --> pdb=" O MET A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1521 Processing helix chain 'A' and resid 1541 through 1560 Processing helix chain 'A' and resid 1580 through 1595 removed outlier: 3.891A pdb=" N VAL A1584 " --> pdb=" O LEU A1580 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ALA A1585 " --> pdb=" O ARG A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1605 removed outlier: 4.316A pdb=" N ILE A1604 " --> pdb=" O ASP A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1631 Processing helix chain 'A' and resid 1635 through 1643 removed outlier: 4.779A pdb=" N ILE A1639 " --> pdb=" O PRO A1635 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A1643 " --> pdb=" O ILE A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1650 Processing helix chain 'A' and resid 1651 through 1669 removed outlier: 3.936A pdb=" N GLN A1666 " --> pdb=" O LEU A1662 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE A1667 " --> pdb=" O LEU A1663 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA A1668 " --> pdb=" O ALA A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1682 Processing helix chain 'A' and resid 1703 through 1715 Processing helix chain 'A' and resid 1731 through 1737 Processing helix chain 'A' and resid 1979 through 2001 removed outlier: 4.330A pdb=" N ARG A1999 " --> pdb=" O ALA A1995 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A2000 " --> pdb=" O SER A1996 " (cutoff:3.500A) Processing helix chain 'A' and resid 2011 through 2030 Proline residue: A2015 - end of helix Proline residue: A2018 - end of helix Processing helix chain 'A' and resid 2033 through 2039 Processing helix chain 'A' and resid 2052 through 2068 removed outlier: 4.788A pdb=" N SER A2056 " --> pdb=" O ASP A2052 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A2065 " --> pdb=" O LEU A2061 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP A2068 " --> pdb=" O LEU A2064 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2076 removed outlier: 4.721A pdb=" N ASP A2073 " --> pdb=" O GLU A2069 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA A2074 " --> pdb=" O GLY A2070 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP A2075 " --> pdb=" O ASP A2071 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2084 removed outlier: 4.525A pdb=" N PHE A2083 " --> pdb=" O LEU A2079 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU A2084 " --> pdb=" O ALA A2080 " (cutoff:3.500A) Processing helix chain 'A' and resid 2087 through 2105 Processing helix chain 'A' and resid 2106 through 2122 removed outlier: 4.220A pdb=" N ASN A2122 " --> pdb=" O ALA A2118 " (cutoff:3.500A) Processing helix chain 'A' and resid 2142 through 2155 Processing helix chain 'A' and resid 2166 through 2181 Processing helix chain 'A' and resid 2196 through 2209 Processing helix chain 'A' and resid 2246 through 2273 removed outlier: 4.086A pdb=" N GLU A2251 " --> pdb=" O GLY A2247 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET A2254 " --> pdb=" O ALA A2250 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA A2260 " --> pdb=" O VAL A2256 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY A2272 " --> pdb=" O LEU A2268 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A2273 " --> pdb=" O SER A2269 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2308 Processing helix chain 'A' and resid 2321 through 2329 Processing helix chain 'A' and resid 2330 through 2336 removed outlier: 4.093A pdb=" N ALA A2334 " --> pdb=" O SER A2330 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG A2335 " --> pdb=" O SER A2331 " (cutoff:3.500A) Processing helix chain 'A' and resid 2355 through 2366 Processing helix chain 'A' and resid 2371 through 2384 removed outlier: 5.390A pdb=" N LEU A2382 " --> pdb=" O LEU A2378 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N CYS A2383 " --> pdb=" O LEU A2379 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP A2384 " --> pdb=" O LEU A2380 " (cutoff:3.500A) Processing helix chain 'A' and resid 2385 through 2394 removed outlier: 4.024A pdb=" N ARG A2393 " --> pdb=" O VAL A2389 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A2394 " --> pdb=" O ALA A2390 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2429 removed outlier: 3.868A pdb=" N LYS A2417 " --> pdb=" O GLU A2413 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A2424 " --> pdb=" O GLU A2420 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA A2425 " --> pdb=" O GLN A2421 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A2426 " --> pdb=" O MET A2422 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A2427 " --> pdb=" O SER A2423 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A2428 " --> pdb=" O ALA A2424 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A2429 " --> pdb=" O ALA A2425 " (cutoff:3.500A) Processing helix chain 'A' and resid 2462 through 2467 removed outlier: 4.438A pdb=" N LEU A2466 " --> pdb=" O ASP A2462 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A2467 " --> pdb=" O PRO A2463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2462 through 2467' Processing helix chain 'A' and resid 2480 through 2490 Processing helix chain 'A' and resid 2494 through 2506 removed outlier: 3.600A pdb=" N GLY A2506 " --> pdb=" O ALA A2502 " (cutoff:3.500A) Processing helix chain 'A' and resid 2528 through 2536 removed outlier: 3.600A pdb=" N LEU A2532 " --> pdb=" O ASP A2528 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL A2533 " --> pdb=" O GLU A2529 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN A2534 " --> pdb=" O SER A2530 " (cutoff:3.500A) Processing helix chain 'A' and resid 2537 through 2545 removed outlier: 5.080A pdb=" N GLY A2545 " --> pdb=" O VAL A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2579 through 2589 removed outlier: 4.984A pdb=" N PHE A2589 " --> pdb=" O ALA A2585 " (cutoff:3.500A) Processing helix chain 'A' and resid 2636 through 2641 removed outlier: 4.588A pdb=" N TRP A2640 " --> pdb=" O ASP A2636 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY A2641 " --> pdb=" O PRO A2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2636 through 2641' Processing helix chain 'A' and resid 2643 through 2650 Processing helix chain 'A' and resid 2651 through 2669 Processing helix chain 'A' and resid 2671 through 2679 removed outlier: 3.852A pdb=" N VAL A2675 " --> pdb=" O SER A2671 " (cutoff:3.500A) Processing helix chain 'A' and resid 2680 through 2685 removed outlier: 4.234A pdb=" N VAL A2684 " --> pdb=" O HIS A2680 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ALA A2685 " --> pdb=" O PRO A2681 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2680 through 2685' Processing helix chain 'A' and resid 2694 through 2708 Processing helix chain 'A' and resid 2714 through 2719 Processing helix chain 'A' and resid 2720 through 2732 removed outlier: 3.805A pdb=" N ILE A2724 " --> pdb=" O LEU A2720 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A2725 " --> pdb=" O PRO A2721 " (cutoff:3.500A) Processing helix chain 'A' and resid 2747 through 2763 Processing helix chain 'A' and resid 2777 through 2788 Processing helix chain 'A' and resid 2792 through 2800 Processing helix chain 'A' and resid 2830 through 2838 Processing helix chain 'A' and resid 2876 through 2886 Processing helix chain 'A' and resid 2904 through 2921 removed outlier: 4.118A pdb=" N ASN A2908 " --> pdb=" O ALA A2904 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A2909 " --> pdb=" O ASN A2905 " (cutoff:3.500A) Processing helix chain 'A' and resid 2933 through 2938 Processing helix chain 'A' and resid 2943 through 2959 removed outlier: 4.230A pdb=" N PHE A2947 " --> pdb=" O GLY A2943 " (cutoff:3.500A) Processing helix chain 'A' and resid 2971 through 2976 removed outlier: 4.428A pdb=" N ALA A2975 " --> pdb=" O ASP A2971 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY A2976 " --> pdb=" O ASP A2972 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2971 through 2976' Processing helix chain 'A' and resid 3016 through 3024 removed outlier: 4.568A pdb=" N PHE A3020 " --> pdb=" O HIS A3016 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A3024 " --> pdb=" O PHE A3020 " (cutoff:3.500A) Processing helix chain 'A' and resid 3025 through 3053 removed outlier: 4.671A pdb=" N ALA A3030 " --> pdb=" O PRO A3026 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 876 removed outlier: 4.997A pdb=" N TRP A 873 " --> pdb=" O ASP A 870 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN A 874 " --> pdb=" O SER A 871 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 875 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 2402 through 2407 removed outlier: 6.555A pdb=" N ALA A2405 " --> pdb=" O GLY A2402 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A2406 " --> pdb=" O GLY A2403 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA A2407 " --> pdb=" O LEU A2404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2402 through 2407' Processing helix chain 'A' and resid 2864 through 2870 removed outlier: 3.765A pdb=" N LEU A2867 " --> pdb=" O LEU A2864 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A2868 " --> pdb=" O GLY A2865 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A2869 " --> pdb=" O ALA A2866 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.594A pdb=" N VAL A 440 " --> pdb=" O MET A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 435 through 440' Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 54 through 67 removed outlier: 4.326A pdb=" N THR B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 84 removed outlier: 3.574A pdb=" N ASP B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 95 removed outlier: 4.611A pdb=" N VAL B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Proline residue: B 95 - end of helix Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.554A pdb=" N TRP B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 122 through 144 Proline residue: B 127 - end of helix removed outlier: 3.855A pdb=" N LEU B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 161 through 171 removed outlier: 4.412A pdb=" N GLY B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 197 removed outlier: 3.872A pdb=" N ALA B 187 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 228 removed outlier: 4.022A pdb=" N ASP B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 276 removed outlier: 4.097A pdb=" N LYS B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 316 removed outlier: 4.340A pdb=" N ILE B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 330 removed outlier: 4.796A pdb=" N ALA B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 347 Processing helix chain 'B' and resid 358 through 369 Proline residue: B 366 - end of helix Processing helix chain 'B' and resid 380 through 389 Processing helix chain 'B' and resid 399 through 405 removed outlier: 4.137A pdb=" N TYR B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 419 through 426 Processing helix chain 'B' and resid 441 through 452 removed outlier: 3.763A pdb=" N GLY B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 493 through 501 Processing helix chain 'B' and resid 505 through 514 Processing helix chain 'B' and resid 528 through 543 removed outlier: 3.647A pdb=" N ILE B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 568 removed outlier: 3.590A pdb=" N VAL B 560 " --> pdb=" O GLN B 556 " (cutoff:3.500A) Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 589 through 605 removed outlier: 5.829A pdb=" N SER B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU B 600 " --> pdb=" O ALA B 596 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG B 604 " --> pdb=" O GLU B 600 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ALA B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 627 removed outlier: 4.003A pdb=" N GLY B 627 " --> pdb=" O GLU B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 634 removed outlier: 4.898A pdb=" N ALA B 632 " --> pdb=" O ARG B 628 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR B 633 " --> pdb=" O TRP B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 651 removed outlier: 5.251A pdb=" N ALA B 649 " --> pdb=" O VAL B 645 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET B 650 " --> pdb=" O GLY B 646 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 645 through 651' Processing helix chain 'B' and resid 658 through 669 removed outlier: 5.784A pdb=" N GLN B 669 " --> pdb=" O LEU B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 713 removed outlier: 3.671A pdb=" N CYS B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 723 removed outlier: 3.554A pdb=" N ALA B 720 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 734 removed outlier: 4.782A pdb=" N ALA B 734 " --> pdb=" O MET B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 removed outlier: 3.686A pdb=" N MET B 744 " --> pdb=" O ASP B 740 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR B 745 " --> pdb=" O VAL B 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 745' Processing helix chain 'B' and resid 746 through 758 Processing helix chain 'B' and resid 776 through 795 Processing helix chain 'B' and resid 809 through 815 Proline residue: B 815 - end of helix Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.797A pdb=" N ARG B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) Proline residue: B 827 - end of helix Processing helix chain 'B' and resid 835 through 848 removed outlier: 4.076A pdb=" N VAL B 839 " --> pdb=" O HIS B 835 " (cutoff:3.500A) Proline residue: B 840 - end of helix removed outlier: 4.278A pdb=" N THR B 848 " --> pdb=" O THR B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 869 Processing helix chain 'B' and resid 881 through 886 removed outlier: 4.077A pdb=" N VAL B 885 " --> pdb=" O ASP B 881 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS B 886 " --> pdb=" O ALA B 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 881 through 886' Processing helix chain 'B' and resid 890 through 898 removed outlier: 4.581A pdb=" N VAL B 894 " --> pdb=" O GLY B 890 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA B 895 " --> pdb=" O THR B 891 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 921 removed outlier: 4.093A pdb=" N ALA B 915 " --> pdb=" O PHE B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 949 removed outlier: 3.651A pdb=" N VAL B 945 " --> pdb=" O GLY B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 968 removed outlier: 4.029A pdb=" N ALA B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1023 removed outlier: 4.780A pdb=" N VAL B1021 " --> pdb=" O PRO B1017 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP B1022 " --> pdb=" O ALA B1018 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY B1023 " --> pdb=" O ASN B1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1017 through 1023' Processing helix chain 'B' and resid 1029 through 1046 Processing helix chain 'B' and resid 1068 through 1080 removed outlier: 4.210A pdb=" N VAL B1072 " --> pdb=" O HIS B1068 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA B1073 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B1078 " --> pdb=" O ASP B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1102 removed outlier: 4.756A pdb=" N VAL B1098 " --> pdb=" O PRO B1094 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLY B1099 " --> pdb=" O ASP B1095 " (cutoff:3.500A) Proline residue: B1100 - end of helix No H-bonds generated for 'chain 'B' and resid 1094 through 1102' Processing helix chain 'B' and resid 1103 through 1112 removed outlier: 3.536A pdb=" N SER B1111 " --> pdb=" O ALA B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1238 Processing helix chain 'B' and resid 1241 through 1246 removed outlier: 4.213A pdb=" N THR B1245 " --> pdb=" O ASN B1241 " (cutoff:3.500A) Processing helix chain 'B' and resid 1247 through 1254 Processing helix chain 'B' and resid 1261 through 1275 Processing helix chain 'B' and resid 1357 through 1364 Processing helix chain 'B' and resid 1365 through 1382 Processing helix chain 'B' and resid 1385 through 1392 Processing helix chain 'B' and resid 1413 through 1436 removed outlier: 4.152A pdb=" N GLY B1436 " --> pdb=" O MET B1432 " (cutoff:3.500A) Processing helix chain 'B' and resid 1448 through 1457 removed outlier: 5.458A pdb=" N TYR B1452 " --> pdb=" O SER B1448 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR B1453 " --> pdb=" O VAL B1449 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1482 removed outlier: 4.024A pdb=" N ASP B1480 " --> pdb=" O SER B1476 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE B1481 " --> pdb=" O LYS B1477 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL B1482 " --> pdb=" O MET B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1508 through 1521 Processing helix chain 'B' and resid 1541 through 1560 Processing helix chain 'B' and resid 1580 through 1595 removed outlier: 3.891A pdb=" N VAL B1584 " --> pdb=" O LEU B1580 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA B1585 " --> pdb=" O ARG B1581 " (cutoff:3.500A) Processing helix chain 'B' and resid 1600 through 1605 removed outlier: 4.317A pdb=" N ILE B1604 " --> pdb=" O ASP B1600 " (cutoff:3.500A) Processing helix chain 'B' and resid 1620 through 1631 Processing helix chain 'B' and resid 1635 through 1643 removed outlier: 4.780A pdb=" N ILE B1639 " --> pdb=" O PRO B1635 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR B1643 " --> pdb=" O ILE B1639 " (cutoff:3.500A) Processing helix chain 'B' and resid 1644 through 1650 Processing helix chain 'B' and resid 1651 through 1669 removed outlier: 3.936A pdb=" N GLN B1666 " --> pdb=" O LEU B1662 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE B1667 " --> pdb=" O LEU B1663 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA B1668 " --> pdb=" O ALA B1664 " (cutoff:3.500A) Processing helix chain 'B' and resid 1672 through 1682 Processing helix chain 'B' and resid 1703 through 1715 Processing helix chain 'B' and resid 1731 through 1737 Processing helix chain 'B' and resid 1979 through 2001 removed outlier: 4.329A pdb=" N ARG B1999 " --> pdb=" O ALA B1995 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU B2000 " --> pdb=" O SER B1996 " (cutoff:3.500A) Processing helix chain 'B' and resid 2011 through 2030 Proline residue: B2015 - end of helix Proline residue: B2018 - end of helix Processing helix chain 'B' and resid 2033 through 2039 Processing helix chain 'B' and resid 2052 through 2068 removed outlier: 4.788A pdb=" N SER B2056 " --> pdb=" O ASP B2052 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP B2065 " --> pdb=" O LEU B2061 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP B2068 " --> pdb=" O LEU B2064 " (cutoff:3.500A) Processing helix chain 'B' and resid 2069 through 2076 removed outlier: 4.721A pdb=" N ASP B2073 " --> pdb=" O GLU B2069 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA B2074 " --> pdb=" O GLY B2070 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP B2075 " --> pdb=" O ASP B2071 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2084 removed outlier: 4.524A pdb=" N PHE B2083 " --> pdb=" O LEU B2079 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU B2084 " --> pdb=" O ALA B2080 " (cutoff:3.500A) Processing helix chain 'B' and resid 2087 through 2105 Processing helix chain 'B' and resid 2106 through 2122 removed outlier: 4.220A pdb=" N ASN B2122 " --> pdb=" O ALA B2118 " (cutoff:3.500A) Processing helix chain 'B' and resid 2142 through 2155 Processing helix chain 'B' and resid 2166 through 2181 Processing helix chain 'B' and resid 2196 through 2209 Processing helix chain 'B' and resid 2246 through 2273 removed outlier: 4.087A pdb=" N GLU B2251 " --> pdb=" O GLY B2247 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET B2254 " --> pdb=" O ALA B2250 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA B2260 " --> pdb=" O VAL B2256 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY B2272 " --> pdb=" O LEU B2268 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA B2273 " --> pdb=" O SER B2269 " (cutoff:3.500A) Processing helix chain 'B' and resid 2297 through 2308 Processing helix chain 'B' and resid 2321 through 2329 Processing helix chain 'B' and resid 2330 through 2336 removed outlier: 4.094A pdb=" N ALA B2334 " --> pdb=" O SER B2330 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG B2335 " --> pdb=" O SER B2331 " (cutoff:3.500A) Processing helix chain 'B' and resid 2355 through 2366 Processing helix chain 'B' and resid 2371 through 2384 removed outlier: 5.390A pdb=" N LEU B2382 " --> pdb=" O LEU B2378 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N CYS B2383 " --> pdb=" O LEU B2379 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP B2384 " --> pdb=" O LEU B2380 " (cutoff:3.500A) Processing helix chain 'B' and resid 2385 through 2394 removed outlier: 4.024A pdb=" N ARG B2393 " --> pdb=" O VAL B2389 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B2394 " --> pdb=" O ALA B2390 " (cutoff:3.500A) Processing helix chain 'B' and resid 2410 through 2429 removed outlier: 3.868A pdb=" N LYS B2417 " --> pdb=" O GLU B2413 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA B2424 " --> pdb=" O GLU B2420 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA B2425 " --> pdb=" O GLN B2421 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA B2426 " --> pdb=" O MET B2422 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B2427 " --> pdb=" O SER B2423 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B2428 " --> pdb=" O ALA B2424 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B2429 " --> pdb=" O ALA B2425 " (cutoff:3.500A) Processing helix chain 'B' and resid 2462 through 2467 removed outlier: 4.438A pdb=" N LEU B2466 " --> pdb=" O ASP B2462 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B2467 " --> pdb=" O PRO B2463 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2462 through 2467' Processing helix chain 'B' and resid 2480 through 2490 Processing helix chain 'B' and resid 2494 through 2506 removed outlier: 3.600A pdb=" N GLY B2506 " --> pdb=" O ALA B2502 " (cutoff:3.500A) Processing helix chain 'B' and resid 2528 through 2536 removed outlier: 3.599A pdb=" N LEU B2532 " --> pdb=" O ASP B2528 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL B2533 " --> pdb=" O GLU B2529 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLN B2534 " --> pdb=" O SER B2530 " (cutoff:3.500A) Processing helix chain 'B' and resid 2537 through 2545 removed outlier: 5.079A pdb=" N GLY B2545 " --> pdb=" O VAL B2541 " (cutoff:3.500A) Processing helix chain 'B' and resid 2579 through 2589 removed outlier: 4.983A pdb=" N PHE B2589 " --> pdb=" O ALA B2585 " (cutoff:3.500A) Processing helix chain 'B' and resid 2636 through 2641 removed outlier: 4.588A pdb=" N TRP B2640 " --> pdb=" O ASP B2636 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY B2641 " --> pdb=" O PRO B2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2636 through 2641' Processing helix chain 'B' and resid 2643 through 2650 Processing helix chain 'B' and resid 2651 through 2669 Processing helix chain 'B' and resid 2671 through 2679 removed outlier: 3.853A pdb=" N VAL B2675 " --> pdb=" O SER B2671 " (cutoff:3.500A) Processing helix chain 'B' and resid 2680 through 2685 removed outlier: 4.234A pdb=" N VAL B2684 " --> pdb=" O HIS B2680 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA B2685 " --> pdb=" O PRO B2681 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2680 through 2685' Processing helix chain 'B' and resid 2694 through 2708 Processing helix chain 'B' and resid 2714 through 2719 Processing helix chain 'B' and resid 2720 through 2732 removed outlier: 3.804A pdb=" N ILE B2724 " --> pdb=" O LEU B2720 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA B2725 " --> pdb=" O PRO B2721 " (cutoff:3.500A) Processing helix chain 'B' and resid 2747 through 2763 Processing helix chain 'B' and resid 2777 through 2788 Processing helix chain 'B' and resid 2792 through 2800 Processing helix chain 'B' and resid 2830 through 2838 Processing helix chain 'B' and resid 2876 through 2886 Processing helix chain 'B' and resid 2904 through 2921 removed outlier: 4.118A pdb=" N ASN B2908 " --> pdb=" O ALA B2904 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B2909 " --> pdb=" O ASN B2905 " (cutoff:3.500A) Processing helix chain 'B' and resid 2933 through 2938 Processing helix chain 'B' and resid 2943 through 2959 removed outlier: 4.230A pdb=" N PHE B2947 " --> pdb=" O GLY B2943 " (cutoff:3.500A) Processing helix chain 'B' and resid 2971 through 2976 removed outlier: 4.427A pdb=" N ALA B2975 " --> pdb=" O ASP B2971 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY B2976 " --> pdb=" O ASP B2972 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2971 through 2976' Processing helix chain 'B' and resid 3016 through 3024 removed outlier: 4.569A pdb=" N PHE B3020 " --> pdb=" O HIS B3016 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B3024 " --> pdb=" O PHE B3020 " (cutoff:3.500A) Processing helix chain 'B' and resid 3025 through 3053 removed outlier: 4.670A pdb=" N ALA B3030 " --> pdb=" O PRO B3026 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 876 removed outlier: 4.997A pdb=" N TRP B 873 " --> pdb=" O ASP B 870 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN B 874 " --> pdb=" O SER B 871 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B 875 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 2402 through 2407 removed outlier: 6.556A pdb=" N ALA B2405 " --> pdb=" O GLY B2402 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU B2406 " --> pdb=" O GLY B2403 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B2407 " --> pdb=" O LEU B2404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2402 through 2407' Processing helix chain 'B' and resid 2864 through 2870 removed outlier: 3.765A pdb=" N LEU B2867 " --> pdb=" O LEU B2864 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B2868 " --> pdb=" O GLY B2865 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA B2869 " --> pdb=" O ALA B2866 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.593A pdb=" N VAL B 440 " --> pdb=" O MET B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 435 through 440' Processing helix chain 'C' and resid 32 through 41 Processing helix chain 'C' and resid 54 through 67 removed outlier: 4.326A pdb=" N THR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 84 removed outlier: 3.574A pdb=" N ASP C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 95 removed outlier: 4.611A pdb=" N VAL C 93 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Proline residue: C 95 - end of helix Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.554A pdb=" N TRP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 121 Processing helix chain 'C' and resid 122 through 144 Proline residue: C 127 - end of helix removed outlier: 3.855A pdb=" N LEU C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 151 Proline residue: C 151 - end of helix Processing helix chain 'C' and resid 161 through 171 removed outlier: 4.413A pdb=" N GLY C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 197 removed outlier: 3.871A pdb=" N ALA C 187 " --> pdb=" O GLN C 183 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 228 removed outlier: 4.021A pdb=" N ASP C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 276 removed outlier: 4.096A pdb=" N LYS C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 316 removed outlier: 4.339A pdb=" N ILE C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 330 removed outlier: 4.796A pdb=" N ALA C 322 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 347 Processing helix chain 'C' and resid 358 through 369 Proline residue: C 366 - end of helix Processing helix chain 'C' and resid 380 through 389 Processing helix chain 'C' and resid 399 through 405 removed outlier: 4.137A pdb=" N TYR C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 419 through 426 Processing helix chain 'C' and resid 441 through 452 removed outlier: 3.762A pdb=" N GLY C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 479 Processing helix chain 'C' and resid 493 through 501 Processing helix chain 'C' and resid 505 through 514 Processing helix chain 'C' and resid 528 through 543 removed outlier: 3.646A pdb=" N ILE C 542 " --> pdb=" O GLU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 568 removed outlier: 3.590A pdb=" N VAL C 560 " --> pdb=" O GLN C 556 " (cutoff:3.500A) Proline residue: C 568 - end of helix Processing helix chain 'C' and resid 589 through 605 removed outlier: 5.828A pdb=" N SER C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU C 600 " --> pdb=" O ALA C 596 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG C 604 " --> pdb=" O GLU C 600 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 627 removed outlier: 4.003A pdb=" N GLY C 627 " --> pdb=" O GLU C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 634 removed outlier: 4.898A pdb=" N ALA C 632 " --> pdb=" O ARG C 628 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR C 633 " --> pdb=" O TRP C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 651 removed outlier: 5.251A pdb=" N ALA C 649 " --> pdb=" O VAL C 645 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET C 650 " --> pdb=" O GLY C 646 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA C 651 " --> pdb=" O THR C 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 645 through 651' Processing helix chain 'C' and resid 658 through 669 removed outlier: 5.784A pdb=" N GLN C 669 " --> pdb=" O LEU C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 713 removed outlier: 3.670A pdb=" N CYS C 705 " --> pdb=" O SER C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 723 removed outlier: 3.553A pdb=" N ALA C 720 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 734 removed outlier: 4.783A pdb=" N ALA C 734 " --> pdb=" O MET C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 745 removed outlier: 3.687A pdb=" N MET C 744 " --> pdb=" O ASP C 740 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR C 745 " --> pdb=" O VAL C 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 745' Processing helix chain 'C' and resid 746 through 758 Processing helix chain 'C' and resid 776 through 795 Processing helix chain 'C' and resid 809 through 815 Proline residue: C 815 - end of helix Processing helix chain 'C' and resid 816 through 827 removed outlier: 3.797A pdb=" N ARG C 825 " --> pdb=" O ALA C 821 " (cutoff:3.500A) Proline residue: C 827 - end of helix Processing helix chain 'C' and resid 835 through 848 removed outlier: 4.077A pdb=" N VAL C 839 " --> pdb=" O HIS C 835 " (cutoff:3.500A) Proline residue: C 840 - end of helix removed outlier: 4.277A pdb=" N THR C 848 " --> pdb=" O THR C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 869 Processing helix chain 'C' and resid 881 through 886 removed outlier: 4.078A pdb=" N VAL C 885 " --> pdb=" O ASP C 881 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS C 886 " --> pdb=" O ALA C 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 881 through 886' Processing helix chain 'C' and resid 890 through 898 removed outlier: 4.580A pdb=" N VAL C 894 " --> pdb=" O GLY C 890 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA C 895 " --> pdb=" O THR C 891 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THR C 898 " --> pdb=" O VAL C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 921 removed outlier: 4.094A pdb=" N ALA C 915 " --> pdb=" O PHE C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 949 removed outlier: 3.651A pdb=" N VAL C 945 " --> pdb=" O GLY C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 968 removed outlier: 4.030A pdb=" N ALA C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1023 removed outlier: 4.780A pdb=" N VAL C1021 " --> pdb=" O PRO C1017 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP C1022 " --> pdb=" O ALA C1018 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY C1023 " --> pdb=" O ASN C1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1017 through 1023' Processing helix chain 'C' and resid 1029 through 1046 Processing helix chain 'C' and resid 1068 through 1080 removed outlier: 4.210A pdb=" N VAL C1072 " --> pdb=" O HIS C1068 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C1073 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C1078 " --> pdb=" O ASP C1074 " (cutoff:3.500A) Processing helix chain 'C' and resid 1094 through 1102 removed outlier: 4.755A pdb=" N VAL C1098 " --> pdb=" O PRO C1094 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLY C1099 " --> pdb=" O ASP C1095 " (cutoff:3.500A) Proline residue: C1100 - end of helix No H-bonds generated for 'chain 'C' and resid 1094 through 1102' Processing helix chain 'C' and resid 1103 through 1112 removed outlier: 3.535A pdb=" N SER C1111 " --> pdb=" O ALA C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1238 Processing helix chain 'C' and resid 1241 through 1246 removed outlier: 4.213A pdb=" N THR C1245 " --> pdb=" O ASN C1241 " (cutoff:3.500A) Processing helix chain 'C' and resid 1247 through 1254 Processing helix chain 'C' and resid 1261 through 1275 Processing helix chain 'C' and resid 1357 through 1364 Processing helix chain 'C' and resid 1365 through 1382 Processing helix chain 'C' and resid 1385 through 1392 Processing helix chain 'C' and resid 1413 through 1436 removed outlier: 4.153A pdb=" N GLY C1436 " --> pdb=" O MET C1432 " (cutoff:3.500A) Processing helix chain 'C' and resid 1448 through 1457 removed outlier: 5.458A pdb=" N TYR C1452 " --> pdb=" O SER C1448 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR C1453 " --> pdb=" O VAL C1449 " (cutoff:3.500A) Processing helix chain 'C' and resid 1463 through 1482 removed outlier: 4.024A pdb=" N ASP C1480 " --> pdb=" O SER C1476 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE C1481 " --> pdb=" O LYS C1477 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL C1482 " --> pdb=" O MET C1478 " (cutoff:3.500A) Processing helix chain 'C' and resid 1508 through 1521 Processing helix chain 'C' and resid 1541 through 1560 Processing helix chain 'C' and resid 1580 through 1595 removed outlier: 3.892A pdb=" N VAL C1584 " --> pdb=" O LEU C1580 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA C1585 " --> pdb=" O ARG C1581 " (cutoff:3.500A) Processing helix chain 'C' and resid 1600 through 1605 removed outlier: 4.317A pdb=" N ILE C1604 " --> pdb=" O ASP C1600 " (cutoff:3.500A) Processing helix chain 'C' and resid 1620 through 1631 Processing helix chain 'C' and resid 1635 through 1643 removed outlier: 4.780A pdb=" N ILE C1639 " --> pdb=" O PRO C1635 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR C1643 " --> pdb=" O ILE C1639 " (cutoff:3.500A) Processing helix chain 'C' and resid 1644 through 1650 Processing helix chain 'C' and resid 1651 through 1669 removed outlier: 3.936A pdb=" N GLN C1666 " --> pdb=" O LEU C1662 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE C1667 " --> pdb=" O LEU C1663 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA C1668 " --> pdb=" O ALA C1664 " (cutoff:3.500A) Processing helix chain 'C' and resid 1672 through 1682 Processing helix chain 'C' and resid 1703 through 1715 Processing helix chain 'C' and resid 1731 through 1737 Processing helix chain 'C' and resid 1979 through 2001 removed outlier: 4.330A pdb=" N ARG C1999 " --> pdb=" O ALA C1995 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU C2000 " --> pdb=" O SER C1996 " (cutoff:3.500A) Processing helix chain 'C' and resid 2011 through 2030 Proline residue: C2015 - end of helix Proline residue: C2018 - end of helix Processing helix chain 'C' and resid 2033 through 2039 Processing helix chain 'C' and resid 2052 through 2068 removed outlier: 4.788A pdb=" N SER C2056 " --> pdb=" O ASP C2052 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP C2065 " --> pdb=" O LEU C2061 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP C2068 " --> pdb=" O LEU C2064 " (cutoff:3.500A) Processing helix chain 'C' and resid 2069 through 2076 removed outlier: 4.721A pdb=" N ASP C2073 " --> pdb=" O GLU C2069 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA C2074 " --> pdb=" O GLY C2070 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP C2075 " --> pdb=" O ASP C2071 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2084 removed outlier: 4.525A pdb=" N PHE C2083 " --> pdb=" O LEU C2079 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU C2084 " --> pdb=" O ALA C2080 " (cutoff:3.500A) Processing helix chain 'C' and resid 2087 through 2105 Processing helix chain 'C' and resid 2106 through 2122 removed outlier: 4.220A pdb=" N ASN C2122 " --> pdb=" O ALA C2118 " (cutoff:3.500A) Processing helix chain 'C' and resid 2142 through 2155 Processing helix chain 'C' and resid 2166 through 2181 Processing helix chain 'C' and resid 2196 through 2209 Processing helix chain 'C' and resid 2246 through 2273 removed outlier: 4.087A pdb=" N GLU C2251 " --> pdb=" O GLY C2247 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET C2254 " --> pdb=" O ALA C2250 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA C2260 " --> pdb=" O VAL C2256 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY C2272 " --> pdb=" O LEU C2268 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA C2273 " --> pdb=" O SER C2269 " (cutoff:3.500A) Processing helix chain 'C' and resid 2297 through 2308 Processing helix chain 'C' and resid 2321 through 2329 Processing helix chain 'C' and resid 2330 through 2336 removed outlier: 4.093A pdb=" N ALA C2334 " --> pdb=" O SER C2330 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG C2335 " --> pdb=" O SER C2331 " (cutoff:3.500A) Processing helix chain 'C' and resid 2355 through 2366 Processing helix chain 'C' and resid 2371 through 2384 removed outlier: 5.390A pdb=" N LEU C2382 " --> pdb=" O LEU C2378 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N CYS C2383 " --> pdb=" O LEU C2379 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP C2384 " --> pdb=" O LEU C2380 " (cutoff:3.500A) Processing helix chain 'C' and resid 2385 through 2394 removed outlier: 4.025A pdb=" N ARG C2393 " --> pdb=" O VAL C2389 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C2394 " --> pdb=" O ALA C2390 " (cutoff:3.500A) Processing helix chain 'C' and resid 2410 through 2429 removed outlier: 3.869A pdb=" N LYS C2417 " --> pdb=" O GLU C2413 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA C2424 " --> pdb=" O GLU C2420 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA C2425 " --> pdb=" O GLN C2421 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C2426 " --> pdb=" O MET C2422 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C2427 " --> pdb=" O SER C2423 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C2428 " --> pdb=" O ALA C2424 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP C2429 " --> pdb=" O ALA C2425 " (cutoff:3.500A) Processing helix chain 'C' and resid 2462 through 2467 removed outlier: 4.439A pdb=" N LEU C2466 " --> pdb=" O ASP C2462 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL C2467 " --> pdb=" O PRO C2463 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2462 through 2467' Processing helix chain 'C' and resid 2480 through 2490 Processing helix chain 'C' and resid 2494 through 2506 removed outlier: 3.601A pdb=" N GLY C2506 " --> pdb=" O ALA C2502 " (cutoff:3.500A) Processing helix chain 'C' and resid 2528 through 2536 removed outlier: 3.600A pdb=" N LEU C2532 " --> pdb=" O ASP C2528 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL C2533 " --> pdb=" O GLU C2529 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN C2534 " --> pdb=" O SER C2530 " (cutoff:3.500A) Processing helix chain 'C' and resid 2537 through 2545 removed outlier: 5.079A pdb=" N GLY C2545 " --> pdb=" O VAL C2541 " (cutoff:3.500A) Processing helix chain 'C' and resid 2579 through 2589 removed outlier: 4.983A pdb=" N PHE C2589 " --> pdb=" O ALA C2585 " (cutoff:3.500A) Processing helix chain 'C' and resid 2636 through 2641 removed outlier: 4.588A pdb=" N TRP C2640 " --> pdb=" O ASP C2636 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY C2641 " --> pdb=" O PRO C2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2636 through 2641' Processing helix chain 'C' and resid 2643 through 2650 Processing helix chain 'C' and resid 2651 through 2669 Processing helix chain 'C' and resid 2671 through 2679 removed outlier: 3.853A pdb=" N VAL C2675 " --> pdb=" O SER C2671 " (cutoff:3.500A) Processing helix chain 'C' and resid 2680 through 2685 removed outlier: 4.235A pdb=" N VAL C2684 " --> pdb=" O HIS C2680 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA C2685 " --> pdb=" O PRO C2681 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2680 through 2685' Processing helix chain 'C' and resid 2694 through 2708 Processing helix chain 'C' and resid 2714 through 2719 Processing helix chain 'C' and resid 2720 through 2732 removed outlier: 3.805A pdb=" N ILE C2724 " --> pdb=" O LEU C2720 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA C2725 " --> pdb=" O PRO C2721 " (cutoff:3.500A) Processing helix chain 'C' and resid 2747 through 2763 Processing helix chain 'C' and resid 2777 through 2788 Processing helix chain 'C' and resid 2792 through 2800 Processing helix chain 'C' and resid 2830 through 2838 Processing helix chain 'C' and resid 2876 through 2886 Processing helix chain 'C' and resid 2904 through 2921 removed outlier: 4.119A pdb=" N ASN C2908 " --> pdb=" O ALA C2904 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C2909 " --> pdb=" O ASN C2905 " (cutoff:3.500A) Processing helix chain 'C' and resid 2933 through 2938 Processing helix chain 'C' and resid 2943 through 2959 removed outlier: 4.231A pdb=" N PHE C2947 " --> pdb=" O GLY C2943 " (cutoff:3.500A) Processing helix chain 'C' and resid 2971 through 2976 removed outlier: 4.427A pdb=" N ALA C2975 " --> pdb=" O ASP C2971 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY C2976 " --> pdb=" O ASP C2972 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2971 through 2976' Processing helix chain 'C' and resid 3016 through 3024 removed outlier: 4.568A pdb=" N PHE C3020 " --> pdb=" O HIS C3016 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU C3024 " --> pdb=" O PHE C3020 " (cutoff:3.500A) Processing helix chain 'C' and resid 3025 through 3053 removed outlier: 4.671A pdb=" N ALA C3030 " --> pdb=" O PRO C3026 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 876 removed outlier: 4.996A pdb=" N TRP C 873 " --> pdb=" O ASP C 870 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN C 874 " --> pdb=" O SER C 871 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 875 " --> pdb=" O LEU C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 2402 through 2407 removed outlier: 6.555A pdb=" N ALA C2405 " --> pdb=" O GLY C2402 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU C2406 " --> pdb=" O GLY C2403 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA C2407 " --> pdb=" O LEU C2404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2402 through 2407' Processing helix chain 'C' and resid 2864 through 2870 removed outlier: 3.765A pdb=" N LEU C2867 " --> pdb=" O LEU C2864 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY C2868 " --> pdb=" O GLY C2865 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA C2869 " --> pdb=" O ALA C2866 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.593A pdb=" N VAL C 440 " --> pdb=" O MET C 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 440' Processing helix chain 'D' and resid 32 through 41 Processing helix chain 'D' and resid 54 through 67 removed outlier: 4.325A pdb=" N THR D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 84 removed outlier: 3.574A pdb=" N ASP D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 95 removed outlier: 4.611A pdb=" N VAL D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Proline residue: D 95 - end of helix Processing helix chain 'D' and resid 99 through 110 removed outlier: 3.553A pdb=" N TRP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 121 Processing helix chain 'D' and resid 122 through 144 Proline residue: D 127 - end of helix removed outlier: 3.854A pdb=" N LEU D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 161 through 171 removed outlier: 4.412A pdb=" N GLY D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 197 removed outlier: 3.872A pdb=" N ALA D 187 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 228 removed outlier: 4.022A pdb=" N ASP D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 276 removed outlier: 4.096A pdb=" N LYS D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 316 removed outlier: 4.340A pdb=" N ILE D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY D 316 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 330 removed outlier: 4.796A pdb=" N ALA D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 347 Processing helix chain 'D' and resid 358 through 369 Proline residue: D 366 - end of helix Processing helix chain 'D' and resid 380 through 389 Processing helix chain 'D' and resid 399 through 405 removed outlier: 4.137A pdb=" N TYR D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 419 through 426 Processing helix chain 'D' and resid 441 through 452 removed outlier: 3.762A pdb=" N GLY D 452 " --> pdb=" O ALA D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 479 Processing helix chain 'D' and resid 493 through 501 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 528 through 543 removed outlier: 3.646A pdb=" N ILE D 542 " --> pdb=" O GLU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 568 removed outlier: 3.589A pdb=" N VAL D 560 " --> pdb=" O GLN D 556 " (cutoff:3.500A) Proline residue: D 568 - end of helix Processing helix chain 'D' and resid 589 through 605 removed outlier: 5.828A pdb=" N SER D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU D 600 " --> pdb=" O ALA D 596 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG D 604 " --> pdb=" O GLU D 600 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 627 removed outlier: 4.002A pdb=" N GLY D 627 " --> pdb=" O GLU D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 634 removed outlier: 4.898A pdb=" N ALA D 632 " --> pdb=" O ARG D 628 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR D 633 " --> pdb=" O TRP D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 651 removed outlier: 5.252A pdb=" N ALA D 649 " --> pdb=" O VAL D 645 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET D 650 " --> pdb=" O GLY D 646 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA D 651 " --> pdb=" O THR D 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 645 through 651' Processing helix chain 'D' and resid 658 through 669 removed outlier: 5.784A pdb=" N GLN D 669 " --> pdb=" O LEU D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 713 removed outlier: 3.671A pdb=" N CYS D 705 " --> pdb=" O SER D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 723 removed outlier: 3.553A pdb=" N ALA D 720 " --> pdb=" O ALA D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 734 removed outlier: 4.783A pdb=" N ALA D 734 " --> pdb=" O MET D 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 745 removed outlier: 3.686A pdb=" N MET D 744 " --> pdb=" O ASP D 740 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR D 745 " --> pdb=" O VAL D 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 745' Processing helix chain 'D' and resid 746 through 758 Processing helix chain 'D' and resid 776 through 795 Processing helix chain 'D' and resid 809 through 815 Proline residue: D 815 - end of helix Processing helix chain 'D' and resid 816 through 827 removed outlier: 3.798A pdb=" N ARG D 825 " --> pdb=" O ALA D 821 " (cutoff:3.500A) Proline residue: D 827 - end of helix Processing helix chain 'D' and resid 835 through 848 removed outlier: 4.076A pdb=" N VAL D 839 " --> pdb=" O HIS D 835 " (cutoff:3.500A) Proline residue: D 840 - end of helix removed outlier: 4.277A pdb=" N THR D 848 " --> pdb=" O THR D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 869 Processing helix chain 'D' and resid 881 through 886 removed outlier: 4.077A pdb=" N VAL D 885 " --> pdb=" O ASP D 881 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS D 886 " --> pdb=" O ALA D 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 881 through 886' Processing helix chain 'D' and resid 890 through 898 removed outlier: 4.581A pdb=" N VAL D 894 " --> pdb=" O GLY D 890 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA D 895 " --> pdb=" O THR D 891 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR D 898 " --> pdb=" O VAL D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 921 removed outlier: 4.094A pdb=" N ALA D 915 " --> pdb=" O PHE D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 949 removed outlier: 3.652A pdb=" N VAL D 945 " --> pdb=" O GLY D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 968 removed outlier: 4.029A pdb=" N ALA D 967 " --> pdb=" O VAL D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1023 removed outlier: 4.780A pdb=" N VAL D1021 " --> pdb=" O PRO D1017 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP D1022 " --> pdb=" O ALA D1018 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY D1023 " --> pdb=" O ASN D1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1017 through 1023' Processing helix chain 'D' and resid 1029 through 1046 Processing helix chain 'D' and resid 1068 through 1080 removed outlier: 4.210A pdb=" N VAL D1072 " --> pdb=" O HIS D1068 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D1073 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D1078 " --> pdb=" O ASP D1074 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1102 removed outlier: 4.755A pdb=" N VAL D1098 " --> pdb=" O PRO D1094 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLY D1099 " --> pdb=" O ASP D1095 " (cutoff:3.500A) Proline residue: D1100 - end of helix No H-bonds generated for 'chain 'D' and resid 1094 through 1102' Processing helix chain 'D' and resid 1103 through 1112 removed outlier: 3.536A pdb=" N SER D1111 " --> pdb=" O ALA D1107 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1238 Processing helix chain 'D' and resid 1241 through 1246 removed outlier: 4.213A pdb=" N THR D1245 " --> pdb=" O ASN D1241 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1254 Processing helix chain 'D' and resid 1261 through 1275 Processing helix chain 'D' and resid 1357 through 1364 Processing helix chain 'D' and resid 1365 through 1382 Processing helix chain 'D' and resid 1385 through 1392 Processing helix chain 'D' and resid 1413 through 1436 removed outlier: 4.153A pdb=" N GLY D1436 " --> pdb=" O MET D1432 " (cutoff:3.500A) Processing helix chain 'D' and resid 1448 through 1457 removed outlier: 5.458A pdb=" N TYR D1452 " --> pdb=" O SER D1448 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR D1453 " --> pdb=" O VAL D1449 " (cutoff:3.500A) Processing helix chain 'D' and resid 1463 through 1482 removed outlier: 4.024A pdb=" N ASP D1480 " --> pdb=" O SER D1476 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE D1481 " --> pdb=" O LYS D1477 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL D1482 " --> pdb=" O MET D1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 1508 through 1521 Processing helix chain 'D' and resid 1541 through 1560 Processing helix chain 'D' and resid 1580 through 1595 removed outlier: 3.892A pdb=" N VAL D1584 " --> pdb=" O LEU D1580 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ALA D1585 " --> pdb=" O ARG D1581 " (cutoff:3.500A) Processing helix chain 'D' and resid 1600 through 1605 removed outlier: 4.317A pdb=" N ILE D1604 " --> pdb=" O ASP D1600 " (cutoff:3.500A) Processing helix chain 'D' and resid 1620 through 1631 Processing helix chain 'D' and resid 1635 through 1643 removed outlier: 4.779A pdb=" N ILE D1639 " --> pdb=" O PRO D1635 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR D1643 " --> pdb=" O ILE D1639 " (cutoff:3.500A) Processing helix chain 'D' and resid 1644 through 1650 Processing helix chain 'D' and resid 1651 through 1669 removed outlier: 3.936A pdb=" N GLN D1666 " --> pdb=" O LEU D1662 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE D1667 " --> pdb=" O LEU D1663 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA D1668 " --> pdb=" O ALA D1664 " (cutoff:3.500A) Processing helix chain 'D' and resid 1672 through 1682 Processing helix chain 'D' and resid 1703 through 1715 Processing helix chain 'D' and resid 1731 through 1737 Processing helix chain 'D' and resid 1979 through 2001 removed outlier: 4.330A pdb=" N ARG D1999 " --> pdb=" O ALA D1995 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU D2000 " --> pdb=" O SER D1996 " (cutoff:3.500A) Processing helix chain 'D' and resid 2011 through 2030 Proline residue: D2015 - end of helix Proline residue: D2018 - end of helix Processing helix chain 'D' and resid 2033 through 2039 Processing helix chain 'D' and resid 2052 through 2068 removed outlier: 4.789A pdb=" N SER D2056 " --> pdb=" O ASP D2052 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP D2065 " --> pdb=" O LEU D2061 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP D2068 " --> pdb=" O LEU D2064 " (cutoff:3.500A) Processing helix chain 'D' and resid 2069 through 2076 removed outlier: 4.721A pdb=" N ASP D2073 " --> pdb=" O GLU D2069 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA D2074 " --> pdb=" O GLY D2070 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP D2075 " --> pdb=" O ASP D2071 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2084 removed outlier: 4.524A pdb=" N PHE D2083 " --> pdb=" O LEU D2079 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU D2084 " --> pdb=" O ALA D2080 " (cutoff:3.500A) Processing helix chain 'D' and resid 2087 through 2105 Processing helix chain 'D' and resid 2106 through 2122 removed outlier: 4.221A pdb=" N ASN D2122 " --> pdb=" O ALA D2118 " (cutoff:3.500A) Processing helix chain 'D' and resid 2142 through 2155 Processing helix chain 'D' and resid 2166 through 2181 Processing helix chain 'D' and resid 2196 through 2209 Processing helix chain 'D' and resid 2246 through 2273 removed outlier: 4.087A pdb=" N GLU D2251 " --> pdb=" O GLY D2247 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET D2254 " --> pdb=" O ALA D2250 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA D2260 " --> pdb=" O VAL D2256 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY D2272 " --> pdb=" O LEU D2268 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA D2273 " --> pdb=" O SER D2269 " (cutoff:3.500A) Processing helix chain 'D' and resid 2297 through 2308 Processing helix chain 'D' and resid 2321 through 2329 Processing helix chain 'D' and resid 2330 through 2336 removed outlier: 4.093A pdb=" N ALA D2334 " --> pdb=" O SER D2330 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG D2335 " --> pdb=" O SER D2331 " (cutoff:3.500A) Processing helix chain 'D' and resid 2355 through 2366 Processing helix chain 'D' and resid 2371 through 2384 removed outlier: 5.390A pdb=" N LEU D2382 " --> pdb=" O LEU D2378 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS D2383 " --> pdb=" O LEU D2379 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP D2384 " --> pdb=" O LEU D2380 " (cutoff:3.500A) Processing helix chain 'D' and resid 2385 through 2394 removed outlier: 4.024A pdb=" N ARG D2393 " --> pdb=" O VAL D2389 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D2394 " --> pdb=" O ALA D2390 " (cutoff:3.500A) Processing helix chain 'D' and resid 2410 through 2429 removed outlier: 3.868A pdb=" N LYS D2417 " --> pdb=" O GLU D2413 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA D2424 " --> pdb=" O GLU D2420 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA D2425 " --> pdb=" O GLN D2421 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D2426 " --> pdb=" O MET D2422 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA D2427 " --> pdb=" O SER D2423 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D2428 " --> pdb=" O ALA D2424 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP D2429 " --> pdb=" O ALA D2425 " (cutoff:3.500A) Processing helix chain 'D' and resid 2462 through 2467 removed outlier: 4.439A pdb=" N LEU D2466 " --> pdb=" O ASP D2462 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL D2467 " --> pdb=" O PRO D2463 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2462 through 2467' Processing helix chain 'D' and resid 2480 through 2490 Processing helix chain 'D' and resid 2494 through 2506 removed outlier: 3.600A pdb=" N GLY D2506 " --> pdb=" O ALA D2502 " (cutoff:3.500A) Processing helix chain 'D' and resid 2528 through 2536 removed outlier: 3.600A pdb=" N LEU D2532 " --> pdb=" O ASP D2528 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL D2533 " --> pdb=" O GLU D2529 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN D2534 " --> pdb=" O SER D2530 " (cutoff:3.500A) Processing helix chain 'D' and resid 2537 through 2545 removed outlier: 5.079A pdb=" N GLY D2545 " --> pdb=" O VAL D2541 " (cutoff:3.500A) Processing helix chain 'D' and resid 2579 through 2589 removed outlier: 4.983A pdb=" N PHE D2589 " --> pdb=" O ALA D2585 " (cutoff:3.500A) Processing helix chain 'D' and resid 2636 through 2641 removed outlier: 4.588A pdb=" N TRP D2640 " --> pdb=" O ASP D2636 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY D2641 " --> pdb=" O PRO D2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2636 through 2641' Processing helix chain 'D' and resid 2643 through 2650 Processing helix chain 'D' and resid 2651 through 2669 Processing helix chain 'D' and resid 2671 through 2679 removed outlier: 3.853A pdb=" N VAL D2675 " --> pdb=" O SER D2671 " (cutoff:3.500A) Processing helix chain 'D' and resid 2680 through 2685 removed outlier: 4.234A pdb=" N VAL D2684 " --> pdb=" O HIS D2680 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA D2685 " --> pdb=" O PRO D2681 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2680 through 2685' Processing helix chain 'D' and resid 2694 through 2708 Processing helix chain 'D' and resid 2714 through 2719 Processing helix chain 'D' and resid 2720 through 2732 removed outlier: 3.804A pdb=" N ILE D2724 " --> pdb=" O LEU D2720 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA D2725 " --> pdb=" O PRO D2721 " (cutoff:3.500A) Processing helix chain 'D' and resid 2747 through 2763 Processing helix chain 'D' and resid 2777 through 2788 Processing helix chain 'D' and resid 2792 through 2800 Processing helix chain 'D' and resid 2830 through 2838 Processing helix chain 'D' and resid 2876 through 2886 Processing helix chain 'D' and resid 2904 through 2921 removed outlier: 4.119A pdb=" N ASN D2908 " --> pdb=" O ALA D2904 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D2909 " --> pdb=" O ASN D2905 " (cutoff:3.500A) Processing helix chain 'D' and resid 2933 through 2938 Processing helix chain 'D' and resid 2943 through 2959 removed outlier: 4.230A pdb=" N PHE D2947 " --> pdb=" O GLY D2943 " (cutoff:3.500A) Processing helix chain 'D' and resid 2971 through 2976 removed outlier: 4.428A pdb=" N ALA D2975 " --> pdb=" O ASP D2971 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY D2976 " --> pdb=" O ASP D2972 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2971 through 2976' Processing helix chain 'D' and resid 3016 through 3024 removed outlier: 4.569A pdb=" N PHE D3020 " --> pdb=" O HIS D3016 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU D3024 " --> pdb=" O PHE D3020 " (cutoff:3.500A) Processing helix chain 'D' and resid 3025 through 3053 removed outlier: 4.671A pdb=" N ALA D3030 " --> pdb=" O PRO D3026 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 876 removed outlier: 4.997A pdb=" N TRP D 873 " --> pdb=" O ASP D 870 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN D 874 " --> pdb=" O SER D 871 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 875 " --> pdb=" O LEU D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 2402 through 2407 removed outlier: 6.555A pdb=" N ALA D2405 " --> pdb=" O GLY D2402 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU D2406 " --> pdb=" O GLY D2403 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA D2407 " --> pdb=" O LEU D2404 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2402 through 2407' Processing helix chain 'D' and resid 2864 through 2870 removed outlier: 3.765A pdb=" N LEU D2867 " --> pdb=" O LEU D2864 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY D2868 " --> pdb=" O GLY D2865 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA D2869 " --> pdb=" O ALA D2866 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 removed outlier: 3.593A pdb=" N VAL D 440 " --> pdb=" O MET D 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 435 through 440' Processing helix chain 'E' and resid 32 through 41 Processing helix chain 'E' and resid 54 through 67 removed outlier: 4.325A pdb=" N THR E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 84 removed outlier: 3.574A pdb=" N ASP E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 95 removed outlier: 4.611A pdb=" N VAL E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG E 94 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Proline residue: E 95 - end of helix Processing helix chain 'E' and resid 99 through 110 removed outlier: 3.554A pdb=" N TRP E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 121 Processing helix chain 'E' and resid 122 through 144 Proline residue: E 127 - end of helix removed outlier: 3.854A pdb=" N LEU E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 151 Proline residue: E 151 - end of helix Processing helix chain 'E' and resid 161 through 171 removed outlier: 4.412A pdb=" N GLY E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 197 removed outlier: 3.871A pdb=" N ALA E 187 " --> pdb=" O GLN E 183 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 228 removed outlier: 4.021A pdb=" N ASP E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 276 removed outlier: 4.096A pdb=" N LYS E 276 " --> pdb=" O ASP E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 316 removed outlier: 4.339A pdb=" N ILE E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP E 306 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 330 removed outlier: 4.796A pdb=" N ALA E 322 " --> pdb=" O ASP E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 347 Processing helix chain 'E' and resid 358 through 369 Proline residue: E 366 - end of helix Processing helix chain 'E' and resid 380 through 389 Processing helix chain 'E' and resid 399 through 405 removed outlier: 4.137A pdb=" N TYR E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) Proline residue: E 405 - end of helix Processing helix chain 'E' and resid 419 through 426 Processing helix chain 'E' and resid 441 through 452 removed outlier: 3.763A pdb=" N GLY E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 479 Processing helix chain 'E' and resid 493 through 501 Processing helix chain 'E' and resid 505 through 514 Processing helix chain 'E' and resid 528 through 543 removed outlier: 3.647A pdb=" N ILE E 542 " --> pdb=" O GLU E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 568 removed outlier: 3.590A pdb=" N VAL E 560 " --> pdb=" O GLN E 556 " (cutoff:3.500A) Proline residue: E 568 - end of helix Processing helix chain 'E' and resid 589 through 605 removed outlier: 5.828A pdb=" N SER E 599 " --> pdb=" O LEU E 595 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU E 600 " --> pdb=" O ALA E 596 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG E 604 " --> pdb=" O GLU E 600 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ALA E 605 " --> pdb=" O LEU E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 627 removed outlier: 4.003A pdb=" N GLY E 627 " --> pdb=" O GLU E 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 634 removed outlier: 4.898A pdb=" N ALA E 632 " --> pdb=" O ARG E 628 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR E 633 " --> pdb=" O TRP E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 651 removed outlier: 5.251A pdb=" N ALA E 649 " --> pdb=" O VAL E 645 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET E 650 " --> pdb=" O GLY E 646 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA E 651 " --> pdb=" O THR E 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 645 through 651' Processing helix chain 'E' and resid 658 through 669 removed outlier: 5.783A pdb=" N GLN E 669 " --> pdb=" O LEU E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 700 through 713 removed outlier: 3.671A pdb=" N CYS E 705 " --> pdb=" O SER E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 715 through 723 removed outlier: 3.554A pdb=" N ALA E 720 " --> pdb=" O ALA E 716 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 734 removed outlier: 4.784A pdb=" N ALA E 734 " --> pdb=" O MET E 730 " (cutoff:3.500A) Processing helix chain 'E' and resid 740 through 745 removed outlier: 3.686A pdb=" N MET E 744 " --> pdb=" O ASP E 740 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR E 745 " --> pdb=" O VAL E 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 740 through 745' Processing helix chain 'E' and resid 746 through 758 Processing helix chain 'E' and resid 776 through 795 Processing helix chain 'E' and resid 809 through 815 Proline residue: E 815 - end of helix Processing helix chain 'E' and resid 816 through 827 removed outlier: 3.797A pdb=" N ARG E 825 " --> pdb=" O ALA E 821 " (cutoff:3.500A) Proline residue: E 827 - end of helix Processing helix chain 'E' and resid 835 through 848 removed outlier: 4.076A pdb=" N VAL E 839 " --> pdb=" O HIS E 835 " (cutoff:3.500A) Proline residue: E 840 - end of helix removed outlier: 4.278A pdb=" N THR E 848 " --> pdb=" O THR E 844 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 869 Processing helix chain 'E' and resid 881 through 886 removed outlier: 4.077A pdb=" N VAL E 885 " --> pdb=" O ASP E 881 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS E 886 " --> pdb=" O ALA E 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 881 through 886' Processing helix chain 'E' and resid 890 through 898 removed outlier: 4.580A pdb=" N VAL E 894 " --> pdb=" O GLY E 890 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA E 895 " --> pdb=" O THR E 891 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR E 898 " --> pdb=" O VAL E 894 " (cutoff:3.500A) Processing helix chain 'E' and resid 903 through 921 removed outlier: 4.093A pdb=" N ALA E 915 " --> pdb=" O PHE E 911 " (cutoff:3.500A) Processing helix chain 'E' and resid 941 through 949 removed outlier: 3.650A pdb=" N VAL E 945 " --> pdb=" O GLY E 941 " (cutoff:3.500A) Processing helix chain 'E' and resid 961 through 968 removed outlier: 4.029A pdb=" N ALA E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 1017 through 1023 removed outlier: 4.780A pdb=" N VAL E1021 " --> pdb=" O PRO E1017 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP E1022 " --> pdb=" O ALA E1018 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY E1023 " --> pdb=" O ASN E1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1017 through 1023' Processing helix chain 'E' and resid 1029 through 1046 Processing helix chain 'E' and resid 1068 through 1080 removed outlier: 4.210A pdb=" N VAL E1072 " --> pdb=" O HIS E1068 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA E1073 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E1078 " --> pdb=" O ASP E1074 " (cutoff:3.500A) Processing helix chain 'E' and resid 1094 through 1102 removed outlier: 4.756A pdb=" N VAL E1098 " --> pdb=" O PRO E1094 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLY E1099 " --> pdb=" O ASP E1095 " (cutoff:3.500A) Proline residue: E1100 - end of helix No H-bonds generated for 'chain 'E' and resid 1094 through 1102' Processing helix chain 'E' and resid 1103 through 1112 removed outlier: 3.536A pdb=" N SER E1111 " --> pdb=" O ALA E1107 " (cutoff:3.500A) Processing helix chain 'E' and resid 1230 through 1238 Processing helix chain 'E' and resid 1241 through 1246 removed outlier: 4.213A pdb=" N THR E1245 " --> pdb=" O ASN E1241 " (cutoff:3.500A) Processing helix chain 'E' and resid 1247 through 1254 Processing helix chain 'E' and resid 1261 through 1275 Processing helix chain 'E' and resid 1357 through 1364 Processing helix chain 'E' and resid 1365 through 1382 Processing helix chain 'E' and resid 1385 through 1392 Processing helix chain 'E' and resid 1413 through 1436 removed outlier: 4.153A pdb=" N GLY E1436 " --> pdb=" O MET E1432 " (cutoff:3.500A) Processing helix chain 'E' and resid 1448 through 1457 removed outlier: 5.459A pdb=" N TYR E1452 " --> pdb=" O SER E1448 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR E1453 " --> pdb=" O VAL E1449 " (cutoff:3.500A) Processing helix chain 'E' and resid 1463 through 1482 removed outlier: 4.023A pdb=" N ASP E1480 " --> pdb=" O SER E1476 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE E1481 " --> pdb=" O LYS E1477 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL E1482 " --> pdb=" O MET E1478 " (cutoff:3.500A) Processing helix chain 'E' and resid 1508 through 1521 Processing helix chain 'E' and resid 1541 through 1560 Processing helix chain 'E' and resid 1580 through 1595 removed outlier: 3.891A pdb=" N VAL E1584 " --> pdb=" O LEU E1580 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ALA E1585 " --> pdb=" O ARG E1581 " (cutoff:3.500A) Processing helix chain 'E' and resid 1600 through 1605 removed outlier: 4.318A pdb=" N ILE E1604 " --> pdb=" O ASP E1600 " (cutoff:3.500A) Processing helix chain 'E' and resid 1620 through 1631 Processing helix chain 'E' and resid 1635 through 1643 removed outlier: 4.779A pdb=" N ILE E1639 " --> pdb=" O PRO E1635 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR E1643 " --> pdb=" O ILE E1639 " (cutoff:3.500A) Processing helix chain 'E' and resid 1644 through 1650 Processing helix chain 'E' and resid 1651 through 1669 removed outlier: 3.935A pdb=" N GLN E1666 " --> pdb=" O LEU E1662 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE E1667 " --> pdb=" O LEU E1663 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA E1668 " --> pdb=" O ALA E1664 " (cutoff:3.500A) Processing helix chain 'E' and resid 1672 through 1682 Processing helix chain 'E' and resid 1703 through 1715 Processing helix chain 'E' and resid 1731 through 1737 Processing helix chain 'E' and resid 1979 through 2001 removed outlier: 4.330A pdb=" N ARG E1999 " --> pdb=" O ALA E1995 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU E2000 " --> pdb=" O SER E1996 " (cutoff:3.500A) Processing helix chain 'E' and resid 2011 through 2030 Proline residue: E2015 - end of helix Proline residue: E2018 - end of helix Processing helix chain 'E' and resid 2033 through 2039 Processing helix chain 'E' and resid 2052 through 2068 removed outlier: 4.788A pdb=" N SER E2056 " --> pdb=" O ASP E2052 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP E2065 " --> pdb=" O LEU E2061 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP E2068 " --> pdb=" O LEU E2064 " (cutoff:3.500A) Processing helix chain 'E' and resid 2069 through 2076 removed outlier: 4.722A pdb=" N ASP E2073 " --> pdb=" O GLU E2069 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA E2074 " --> pdb=" O GLY E2070 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP E2075 " --> pdb=" O ASP E2071 " (cutoff:3.500A) Processing helix chain 'E' and resid 2077 through 2084 removed outlier: 4.524A pdb=" N PHE E2083 " --> pdb=" O LEU E2079 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU E2084 " --> pdb=" O ALA E2080 " (cutoff:3.500A) Processing helix chain 'E' and resid 2087 through 2105 Processing helix chain 'E' and resid 2106 through 2122 removed outlier: 4.220A pdb=" N ASN E2122 " --> pdb=" O ALA E2118 " (cutoff:3.500A) Processing helix chain 'E' and resid 2142 through 2155 Processing helix chain 'E' and resid 2166 through 2181 Processing helix chain 'E' and resid 2196 through 2209 Processing helix chain 'E' and resid 2246 through 2273 removed outlier: 4.086A pdb=" N GLU E2251 " --> pdb=" O GLY E2247 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET E2254 " --> pdb=" O ALA E2250 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA E2260 " --> pdb=" O VAL E2256 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY E2272 " --> pdb=" O LEU E2268 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA E2273 " --> pdb=" O SER E2269 " (cutoff:3.500A) Processing helix chain 'E' and resid 2297 through 2308 Processing helix chain 'E' and resid 2321 through 2329 Processing helix chain 'E' and resid 2330 through 2336 removed outlier: 4.094A pdb=" N ALA E2334 " --> pdb=" O SER E2330 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG E2335 " --> pdb=" O SER E2331 " (cutoff:3.500A) Processing helix chain 'E' and resid 2355 through 2366 Processing helix chain 'E' and resid 2371 through 2384 removed outlier: 5.391A pdb=" N LEU E2382 " --> pdb=" O LEU E2378 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N CYS E2383 " --> pdb=" O LEU E2379 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP E2384 " --> pdb=" O LEU E2380 " (cutoff:3.500A) Processing helix chain 'E' and resid 2385 through 2394 removed outlier: 4.023A pdb=" N ARG E2393 " --> pdb=" O VAL E2389 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER E2394 " --> pdb=" O ALA E2390 " (cutoff:3.500A) Processing helix chain 'E' and resid 2410 through 2429 removed outlier: 3.868A pdb=" N LYS E2417 " --> pdb=" O GLU E2413 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA E2424 " --> pdb=" O GLU E2420 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA E2425 " --> pdb=" O GLN E2421 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA E2426 " --> pdb=" O MET E2422 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA E2427 " --> pdb=" O SER E2423 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E2428 " --> pdb=" O ALA E2424 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP E2429 " --> pdb=" O ALA E2425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2462 through 2467 removed outlier: 4.439A pdb=" N LEU E2466 " --> pdb=" O ASP E2462 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL E2467 " --> pdb=" O PRO E2463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2462 through 2467' Processing helix chain 'E' and resid 2480 through 2490 Processing helix chain 'E' and resid 2494 through 2506 removed outlier: 3.600A pdb=" N GLY E2506 " --> pdb=" O ALA E2502 " (cutoff:3.500A) Processing helix chain 'E' and resid 2528 through 2536 removed outlier: 3.600A pdb=" N LEU E2532 " --> pdb=" O ASP E2528 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL E2533 " --> pdb=" O GLU E2529 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN E2534 " --> pdb=" O SER E2530 " (cutoff:3.500A) Processing helix chain 'E' and resid 2537 through 2545 removed outlier: 5.080A pdb=" N GLY E2545 " --> pdb=" O VAL E2541 " (cutoff:3.500A) Processing helix chain 'E' and resid 2579 through 2589 removed outlier: 4.983A pdb=" N PHE E2589 " --> pdb=" O ALA E2585 " (cutoff:3.500A) Processing helix chain 'E' and resid 2636 through 2641 removed outlier: 4.588A pdb=" N TRP E2640 " --> pdb=" O ASP E2636 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY E2641 " --> pdb=" O PRO E2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2636 through 2641' Processing helix chain 'E' and resid 2643 through 2650 Processing helix chain 'E' and resid 2651 through 2669 Processing helix chain 'E' and resid 2671 through 2679 removed outlier: 3.853A pdb=" N VAL E2675 " --> pdb=" O SER E2671 " (cutoff:3.500A) Processing helix chain 'E' and resid 2680 through 2685 removed outlier: 4.235A pdb=" N VAL E2684 " --> pdb=" O HIS E2680 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA E2685 " --> pdb=" O PRO E2681 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2680 through 2685' Processing helix chain 'E' and resid 2694 through 2708 Processing helix chain 'E' and resid 2714 through 2719 Processing helix chain 'E' and resid 2720 through 2732 removed outlier: 3.805A pdb=" N ILE E2724 " --> pdb=" O LEU E2720 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA E2725 " --> pdb=" O PRO E2721 " (cutoff:3.500A) Processing helix chain 'E' and resid 2747 through 2763 Processing helix chain 'E' and resid 2777 through 2788 Processing helix chain 'E' and resid 2792 through 2800 Processing helix chain 'E' and resid 2830 through 2838 Processing helix chain 'E' and resid 2876 through 2886 Processing helix chain 'E' and resid 2904 through 2921 removed outlier: 4.119A pdb=" N ASN E2908 " --> pdb=" O ALA E2904 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU E2909 " --> pdb=" O ASN E2905 " (cutoff:3.500A) Processing helix chain 'E' and resid 2933 through 2938 Processing helix chain 'E' and resid 2943 through 2959 removed outlier: 4.230A pdb=" N PHE E2947 " --> pdb=" O GLY E2943 " (cutoff:3.500A) Processing helix chain 'E' and resid 2971 through 2976 removed outlier: 4.428A pdb=" N ALA E2975 " --> pdb=" O ASP E2971 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY E2976 " --> pdb=" O ASP E2972 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2971 through 2976' Processing helix chain 'E' and resid 3016 through 3024 removed outlier: 4.569A pdb=" N PHE E3020 " --> pdb=" O HIS E3016 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU E3024 " --> pdb=" O PHE E3020 " (cutoff:3.500A) Processing helix chain 'E' and resid 3025 through 3053 removed outlier: 4.671A pdb=" N ALA E3030 " --> pdb=" O PRO E3026 " (cutoff:3.500A) Processing helix chain 'E' and resid 870 through 876 removed outlier: 4.997A pdb=" N TRP E 873 " --> pdb=" O ASP E 870 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN E 874 " --> pdb=" O SER E 871 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 875 " --> pdb=" O LEU E 872 " (cutoff:3.500A) Processing helix chain 'E' and resid 2402 through 2407 removed outlier: 6.555A pdb=" N ALA E2405 " --> pdb=" O GLY E2402 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU E2406 " --> pdb=" O GLY E2403 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA E2407 " --> pdb=" O LEU E2404 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2402 through 2407' Processing helix chain 'E' and resid 2864 through 2870 removed outlier: 3.765A pdb=" N LEU E2867 " --> pdb=" O LEU E2864 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY E2868 " --> pdb=" O GLY E2865 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA E2869 " --> pdb=" O ALA E2866 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 440 removed outlier: 3.594A pdb=" N VAL E 440 " --> pdb=" O MET E 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 435 through 440' Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 54 through 67 removed outlier: 4.326A pdb=" N THR F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 84 removed outlier: 3.574A pdb=" N ASP F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 95 removed outlier: 4.611A pdb=" N VAL F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Proline residue: F 95 - end of helix Processing helix chain 'F' and resid 99 through 110 removed outlier: 3.555A pdb=" N TRP F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 121 Processing helix chain 'F' and resid 122 through 144 Proline residue: F 127 - end of helix removed outlier: 3.855A pdb=" N LEU F 130 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 151 Proline residue: F 151 - end of helix Processing helix chain 'F' and resid 161 through 171 removed outlier: 4.412A pdb=" N GLY F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 197 removed outlier: 3.871A pdb=" N ALA F 187 " --> pdb=" O GLN F 183 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 228 removed outlier: 4.021A pdb=" N ASP F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 276 removed outlier: 4.097A pdb=" N LYS F 276 " --> pdb=" O ASP F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 316 removed outlier: 4.339A pdb=" N ILE F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP F 306 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 330 removed outlier: 4.796A pdb=" N ALA F 322 " --> pdb=" O ASP F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 347 Processing helix chain 'F' and resid 358 through 369 Proline residue: F 366 - end of helix Processing helix chain 'F' and resid 380 through 389 Processing helix chain 'F' and resid 399 through 405 removed outlier: 4.137A pdb=" N TYR F 403 " --> pdb=" O ALA F 399 " (cutoff:3.500A) Proline residue: F 405 - end of helix Processing helix chain 'F' and resid 419 through 426 Processing helix chain 'F' and resid 441 through 452 removed outlier: 3.763A pdb=" N GLY F 452 " --> pdb=" O ALA F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 479 Processing helix chain 'F' and resid 493 through 501 Processing helix chain 'F' and resid 505 through 514 Processing helix chain 'F' and resid 528 through 543 removed outlier: 3.646A pdb=" N ILE F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 568 removed outlier: 3.590A pdb=" N VAL F 560 " --> pdb=" O GLN F 556 " (cutoff:3.500A) Proline residue: F 568 - end of helix Processing helix chain 'F' and resid 589 through 605 removed outlier: 5.828A pdb=" N SER F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU F 600 " --> pdb=" O ALA F 596 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG F 604 " --> pdb=" O GLU F 600 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA F 605 " --> pdb=" O LEU F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 617 through 627 removed outlier: 4.003A pdb=" N GLY F 627 " --> pdb=" O GLU F 623 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 634 removed outlier: 4.899A pdb=" N ALA F 632 " --> pdb=" O ARG F 628 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR F 633 " --> pdb=" O TRP F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 651 removed outlier: 5.252A pdb=" N ALA F 649 " --> pdb=" O VAL F 645 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET F 650 " --> pdb=" O GLY F 646 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA F 651 " --> pdb=" O THR F 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 645 through 651' Processing helix chain 'F' and resid 658 through 669 removed outlier: 5.784A pdb=" N GLN F 669 " --> pdb=" O LEU F 665 " (cutoff:3.500A) Processing helix chain 'F' and resid 700 through 713 removed outlier: 3.672A pdb=" N CYS F 705 " --> pdb=" O SER F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 723 removed outlier: 3.554A pdb=" N ALA F 720 " --> pdb=" O ALA F 716 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 734 removed outlier: 4.784A pdb=" N ALA F 734 " --> pdb=" O MET F 730 " (cutoff:3.500A) Processing helix chain 'F' and resid 740 through 745 removed outlier: 3.686A pdb=" N MET F 744 " --> pdb=" O ASP F 740 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR F 745 " --> pdb=" O VAL F 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 740 through 745' Processing helix chain 'F' and resid 746 through 758 Processing helix chain 'F' and resid 776 through 795 Processing helix chain 'F' and resid 809 through 815 Proline residue: F 815 - end of helix Processing helix chain 'F' and resid 816 through 827 removed outlier: 3.798A pdb=" N ARG F 825 " --> pdb=" O ALA F 821 " (cutoff:3.500A) Proline residue: F 827 - end of helix Processing helix chain 'F' and resid 835 through 848 removed outlier: 4.076A pdb=" N VAL F 839 " --> pdb=" O HIS F 835 " (cutoff:3.500A) Proline residue: F 840 - end of helix removed outlier: 4.277A pdb=" N THR F 848 " --> pdb=" O THR F 844 " (cutoff:3.500A) Processing helix chain 'F' and resid 862 through 869 Processing helix chain 'F' and resid 881 through 886 removed outlier: 4.077A pdb=" N VAL F 885 " --> pdb=" O ASP F 881 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS F 886 " --> pdb=" O ALA F 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 881 through 886' Processing helix chain 'F' and resid 890 through 898 removed outlier: 4.580A pdb=" N VAL F 894 " --> pdb=" O GLY F 890 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA F 895 " --> pdb=" O THR F 891 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR F 898 " --> pdb=" O VAL F 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 903 through 921 removed outlier: 4.093A pdb=" N ALA F 915 " --> pdb=" O PHE F 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 941 through 949 removed outlier: 3.652A pdb=" N VAL F 945 " --> pdb=" O GLY F 941 " (cutoff:3.500A) Processing helix chain 'F' and resid 961 through 968 removed outlier: 4.029A pdb=" N ALA F 967 " --> pdb=" O VAL F 963 " (cutoff:3.500A) Processing helix chain 'F' and resid 1017 through 1023 removed outlier: 4.780A pdb=" N VAL F1021 " --> pdb=" O PRO F1017 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP F1022 " --> pdb=" O ALA F1018 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY F1023 " --> pdb=" O ASN F1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1017 through 1023' Processing helix chain 'F' and resid 1029 through 1046 Processing helix chain 'F' and resid 1068 through 1080 removed outlier: 4.210A pdb=" N VAL F1072 " --> pdb=" O HIS F1068 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F1073 " --> pdb=" O PRO F1069 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F1078 " --> pdb=" O ASP F1074 " (cutoff:3.500A) Processing helix chain 'F' and resid 1094 through 1102 removed outlier: 4.755A pdb=" N VAL F1098 " --> pdb=" O PRO F1094 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLY F1099 " --> pdb=" O ASP F1095 " (cutoff:3.500A) Proline residue: F1100 - end of helix No H-bonds generated for 'chain 'F' and resid 1094 through 1102' Processing helix chain 'F' and resid 1103 through 1112 removed outlier: 3.536A pdb=" N SER F1111 " --> pdb=" O ALA F1107 " (cutoff:3.500A) Processing helix chain 'F' and resid 1230 through 1238 Processing helix chain 'F' and resid 1241 through 1246 removed outlier: 4.213A pdb=" N THR F1245 " --> pdb=" O ASN F1241 " (cutoff:3.500A) Processing helix chain 'F' and resid 1247 through 1254 Processing helix chain 'F' and resid 1261 through 1275 Processing helix chain 'F' and resid 1357 through 1364 Processing helix chain 'F' and resid 1365 through 1382 Processing helix chain 'F' and resid 1385 through 1392 Processing helix chain 'F' and resid 1413 through 1436 removed outlier: 4.152A pdb=" N GLY F1436 " --> pdb=" O MET F1432 " (cutoff:3.500A) Processing helix chain 'F' and resid 1448 through 1457 removed outlier: 5.458A pdb=" N TYR F1452 " --> pdb=" O SER F1448 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR F1453 " --> pdb=" O VAL F1449 " (cutoff:3.500A) Processing helix chain 'F' and resid 1463 through 1482 removed outlier: 4.024A pdb=" N ASP F1480 " --> pdb=" O SER F1476 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE F1481 " --> pdb=" O LYS F1477 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL F1482 " --> pdb=" O MET F1478 " (cutoff:3.500A) Processing helix chain 'F' and resid 1508 through 1521 Processing helix chain 'F' and resid 1541 through 1560 Processing helix chain 'F' and resid 1580 through 1595 removed outlier: 3.892A pdb=" N VAL F1584 " --> pdb=" O LEU F1580 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ALA F1585 " --> pdb=" O ARG F1581 " (cutoff:3.500A) Processing helix chain 'F' and resid 1600 through 1605 removed outlier: 4.317A pdb=" N ILE F1604 " --> pdb=" O ASP F1600 " (cutoff:3.500A) Processing helix chain 'F' and resid 1620 through 1631 Processing helix chain 'F' and resid 1635 through 1643 removed outlier: 4.780A pdb=" N ILE F1639 " --> pdb=" O PRO F1635 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR F1643 " --> pdb=" O ILE F1639 " (cutoff:3.500A) Processing helix chain 'F' and resid 1644 through 1650 Processing helix chain 'F' and resid 1651 through 1669 removed outlier: 3.936A pdb=" N GLN F1666 " --> pdb=" O LEU F1662 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE F1667 " --> pdb=" O LEU F1663 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA F1668 " --> pdb=" O ALA F1664 " (cutoff:3.500A) Processing helix chain 'F' and resid 1672 through 1682 Processing helix chain 'F' and resid 1703 through 1715 Processing helix chain 'F' and resid 1731 through 1737 Processing helix chain 'F' and resid 1979 through 2001 removed outlier: 4.329A pdb=" N ARG F1999 " --> pdb=" O ALA F1995 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU F2000 " --> pdb=" O SER F1996 " (cutoff:3.500A) Processing helix chain 'F' and resid 2011 through 2030 Proline residue: F2015 - end of helix Proline residue: F2018 - end of helix Processing helix chain 'F' and resid 2033 through 2039 Processing helix chain 'F' and resid 2052 through 2068 removed outlier: 4.788A pdb=" N SER F2056 " --> pdb=" O ASP F2052 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP F2065 " --> pdb=" O LEU F2061 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP F2068 " --> pdb=" O LEU F2064 " (cutoff:3.500A) Processing helix chain 'F' and resid 2069 through 2076 removed outlier: 4.721A pdb=" N ASP F2073 " --> pdb=" O GLU F2069 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA F2074 " --> pdb=" O GLY F2070 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP F2075 " --> pdb=" O ASP F2071 " (cutoff:3.500A) Processing helix chain 'F' and resid 2077 through 2084 removed outlier: 4.524A pdb=" N PHE F2083 " --> pdb=" O LEU F2079 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU F2084 " --> pdb=" O ALA F2080 " (cutoff:3.500A) Processing helix chain 'F' and resid 2087 through 2105 Processing helix chain 'F' and resid 2106 through 2122 removed outlier: 4.221A pdb=" N ASN F2122 " --> pdb=" O ALA F2118 " (cutoff:3.500A) Processing helix chain 'F' and resid 2142 through 2155 Processing helix chain 'F' and resid 2166 through 2181 Processing helix chain 'F' and resid 2196 through 2209 Processing helix chain 'F' and resid 2246 through 2273 removed outlier: 4.086A pdb=" N GLU F2251 " --> pdb=" O GLY F2247 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET F2254 " --> pdb=" O ALA F2250 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA F2260 " --> pdb=" O VAL F2256 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY F2272 " --> pdb=" O LEU F2268 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA F2273 " --> pdb=" O SER F2269 " (cutoff:3.500A) Processing helix chain 'F' and resid 2297 through 2308 Processing helix chain 'F' and resid 2321 through 2329 Processing helix chain 'F' and resid 2330 through 2336 removed outlier: 4.094A pdb=" N ALA F2334 " --> pdb=" O SER F2330 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG F2335 " --> pdb=" O SER F2331 " (cutoff:3.500A) Processing helix chain 'F' and resid 2355 through 2366 Processing helix chain 'F' and resid 2371 through 2384 removed outlier: 5.390A pdb=" N LEU F2382 " --> pdb=" O LEU F2378 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS F2383 " --> pdb=" O LEU F2379 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP F2384 " --> pdb=" O LEU F2380 " (cutoff:3.500A) Processing helix chain 'F' and resid 2385 through 2394 removed outlier: 4.024A pdb=" N ARG F2393 " --> pdb=" O VAL F2389 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER F2394 " --> pdb=" O ALA F2390 " (cutoff:3.500A) Processing helix chain 'F' and resid 2410 through 2429 removed outlier: 3.868A pdb=" N LYS F2417 " --> pdb=" O GLU F2413 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA F2424 " --> pdb=" O GLU F2420 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA F2425 " --> pdb=" O GLN F2421 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA F2426 " --> pdb=" O MET F2422 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA F2427 " --> pdb=" O SER F2423 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F2428 " --> pdb=" O ALA F2424 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP F2429 " --> pdb=" O ALA F2425 " (cutoff:3.500A) Processing helix chain 'F' and resid 2462 through 2467 removed outlier: 4.438A pdb=" N LEU F2466 " --> pdb=" O ASP F2462 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL F2467 " --> pdb=" O PRO F2463 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2462 through 2467' Processing helix chain 'F' and resid 2480 through 2490 Processing helix chain 'F' and resid 2494 through 2506 removed outlier: 3.600A pdb=" N GLY F2506 " --> pdb=" O ALA F2502 " (cutoff:3.500A) Processing helix chain 'F' and resid 2528 through 2536 removed outlier: 3.600A pdb=" N LEU F2532 " --> pdb=" O ASP F2528 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL F2533 " --> pdb=" O GLU F2529 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN F2534 " --> pdb=" O SER F2530 " (cutoff:3.500A) Processing helix chain 'F' and resid 2537 through 2545 removed outlier: 5.080A pdb=" N GLY F2545 " --> pdb=" O VAL F2541 " (cutoff:3.500A) Processing helix chain 'F' and resid 2579 through 2589 removed outlier: 4.983A pdb=" N PHE F2589 " --> pdb=" O ALA F2585 " (cutoff:3.500A) Processing helix chain 'F' and resid 2636 through 2641 removed outlier: 4.588A pdb=" N TRP F2640 " --> pdb=" O ASP F2636 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY F2641 " --> pdb=" O PRO F2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2636 through 2641' Processing helix chain 'F' and resid 2643 through 2650 Processing helix chain 'F' and resid 2651 through 2669 Processing helix chain 'F' and resid 2671 through 2679 removed outlier: 3.853A pdb=" N VAL F2675 " --> pdb=" O SER F2671 " (cutoff:3.500A) Processing helix chain 'F' and resid 2680 through 2685 removed outlier: 4.235A pdb=" N VAL F2684 " --> pdb=" O HIS F2680 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA F2685 " --> pdb=" O PRO F2681 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2680 through 2685' Processing helix chain 'F' and resid 2694 through 2708 Processing helix chain 'F' and resid 2714 through 2719 Processing helix chain 'F' and resid 2720 through 2732 removed outlier: 3.806A pdb=" N ILE F2724 " --> pdb=" O LEU F2720 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA F2725 " --> pdb=" O PRO F2721 " (cutoff:3.500A) Processing helix chain 'F' and resid 2747 through 2763 Processing helix chain 'F' and resid 2777 through 2788 Processing helix chain 'F' and resid 2792 through 2800 Processing helix chain 'F' and resid 2830 through 2838 Processing helix chain 'F' and resid 2876 through 2886 Processing helix chain 'F' and resid 2904 through 2921 removed outlier: 4.119A pdb=" N ASN F2908 " --> pdb=" O ALA F2904 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU F2909 " --> pdb=" O ASN F2905 " (cutoff:3.500A) Processing helix chain 'F' and resid 2933 through 2938 Processing helix chain 'F' and resid 2943 through 2959 removed outlier: 4.230A pdb=" N PHE F2947 " --> pdb=" O GLY F2943 " (cutoff:3.500A) Processing helix chain 'F' and resid 2971 through 2976 removed outlier: 4.428A pdb=" N ALA F2975 " --> pdb=" O ASP F2971 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY F2976 " --> pdb=" O ASP F2972 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2971 through 2976' Processing helix chain 'F' and resid 3016 through 3024 removed outlier: 4.569A pdb=" N PHE F3020 " --> pdb=" O HIS F3016 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU F3024 " --> pdb=" O PHE F3020 " (cutoff:3.500A) Processing helix chain 'F' and resid 3025 through 3053 removed outlier: 4.671A pdb=" N ALA F3030 " --> pdb=" O PRO F3026 " (cutoff:3.500A) Processing helix chain 'F' and resid 870 through 876 removed outlier: 4.996A pdb=" N TRP F 873 " --> pdb=" O ASP F 870 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN F 874 " --> pdb=" O SER F 871 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA F 875 " --> pdb=" O LEU F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 2402 through 2407 removed outlier: 6.555A pdb=" N ALA F2405 " --> pdb=" O GLY F2402 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU F2406 " --> pdb=" O GLY F2403 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA F2407 " --> pdb=" O LEU F2404 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2402 through 2407' Processing helix chain 'F' and resid 2864 through 2870 removed outlier: 3.765A pdb=" N LEU F2867 " --> pdb=" O LEU F2864 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY F2868 " --> pdb=" O GLY F2865 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA F2869 " --> pdb=" O ALA F2866 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 440 removed outlier: 3.594A pdb=" N VAL F 440 " --> pdb=" O MET F 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 435 through 440' Processing sheet with id= 1, first strand: chain 'A' and resid 153 through 157 removed outlier: 4.026A pdb=" N ALA A 154 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLY A 49 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A 374 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY A 355 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 245 through 249 removed outlier: 5.296A pdb=" N MET A 207 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 406 through 409 Processing sheet with id= 4, first strand: chain 'A' and resid 455 through 459 removed outlier: 3.526A pdb=" N GLY A 459 " --> pdb=" O ASN A 488 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY A 519 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A 547 " --> pdb=" O PRO A 571 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 573 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 577 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 685 through 688 Processing sheet with id= 6, first strand: chain 'A' and resid 800 through 804 removed outlier: 5.854A pdb=" N GLY A 800 " --> pdb=" O ALA A2440 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A2440 " --> pdb=" O GLY A 800 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N THR A 804 " --> pdb=" O GLY A2436 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY A2436 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 951 through 954 removed outlier: 3.679A pdb=" N ARG A 957 " --> pdb=" O TRP A 954 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 972 through 976 removed outlier: 4.642A pdb=" N THR A 994 " --> pdb=" O PRO A 981 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 983 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 990 " --> pdb=" O HIS A 985 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 998 " --> pdb=" O HIS A 995 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 999 " --> pdb=" O PHE A1014 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 1060 through 1067 Processing sheet with id= 10, first strand: chain 'A' and resid 1127 through 1130 removed outlier: 6.682A pdb=" N ARG A1185 " --> pdb=" O LEU A1130 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A1131 " --> pdb=" O ARG A1185 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A1331 " --> pdb=" O ALA A1323 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A1323 " --> pdb=" O MET A1331 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A1337 " --> pdb=" O GLU A1317 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU A1317 " --> pdb=" O LEU A1337 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA A1339 " --> pdb=" O GLY A1315 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLY A1315 " --> pdb=" O ALA A1339 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP A1320 " --> pdb=" O ARG A1309 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG A1309 " --> pdb=" O ASP A1320 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA A1322 " --> pdb=" O VAL A1307 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL A1307 " --> pdb=" O ALA A1322 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 1396 through 1399 removed outlier: 4.691A pdb=" N VAL A1402 " --> pdb=" O ALA A1399 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1524 through 1527 removed outlier: 6.900A pdb=" N ALA A1537 " --> pdb=" O VAL A1527 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER A1534 " --> pdb=" O PRO A1499 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A1494 " --> pdb=" O VAL A1568 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N SER A1564 " --> pdb=" O ARG A1498 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1724 through 1728 Processing sheet with id= 14, first strand: chain 'A' and resid 2047 through 2051 removed outlier: 4.094A pdb=" N LEU A2187 " --> pdb=" O PHE A2050 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A2157 " --> pdb=" O GLU A2131 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A2134 " --> pdb=" O LEU A2230 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 2212 through 2215 removed outlier: 4.090A pdb=" N GLN A2218 " --> pdb=" O LEU A2215 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 2282 through 2288 removed outlier: 3.979A pdb=" N ILE A2396 " --> pdb=" O LEU A2338 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY A2344 " --> pdb=" O LEU A2400 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 2471 through 2476 removed outlier: 3.528A pdb=" N GLY A2471 " --> pdb=" O LEU A2827 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A2827 " --> pdb=" O GLY A2471 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A2822 " --> pdb=" O ASP A2774 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 2594 through 2600 Processing sheet with id= 19, first strand: chain 'A' and resid 2847 through 2853 removed outlier: 4.324A pdb=" N PHE A2847 " --> pdb=" O ALA A3013 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP A2853 " --> pdb=" O HIS A3007 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N HIS A3007 " --> pdb=" O ASP A2853 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE A3005 " --> pdb=" O GLY A3006 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A3008 " --> pdb=" O LEU A3003 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU A3003 " --> pdb=" O VAL A3008 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY A3010 " --> pdb=" O THR A3001 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR A3001 " --> pdb=" O GLY A3010 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A3012 " --> pdb=" O MET A2999 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET A2999 " --> pdb=" O VAL A3012 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A3014 " --> pdb=" O ALA A2997 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA A2997 " --> pdb=" O LEU A3014 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A2894 " --> pdb=" O ALA A2997 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A3001 " --> pdb=" O SER A2896 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS A2898 " --> pdb=" O THR A3001 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU A3003 " --> pdb=" O HIS A2898 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ALA A2893 " --> pdb=" O PRO A2927 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 2960 through 2963 removed outlier: 6.666A pdb=" N ASP A2985 " --> pdb=" O PRO A2963 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'A' and resid 1163 through 1171 Processing sheet with id= 22, first strand: chain 'A' and resid 1220 through 1227 removed outlier: 3.567A pdb=" N ARG A1220 " --> pdb=" O VAL A1307 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP A1301 " --> pdb=" O ALA A1226 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'A' and resid 1342 through 1346 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'B' and resid 153 through 157 removed outlier: 4.027A pdb=" N ALA B 154 " --> pdb=" O TYR B 44 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLY B 49 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 374 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLY B 355 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 245 through 249 removed outlier: 5.295A pdb=" N MET B 207 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 406 through 409 Processing sheet with id= 27, first strand: chain 'B' and resid 455 through 459 removed outlier: 3.525A pdb=" N GLY B 459 " --> pdb=" O ASN B 488 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY B 519 " --> pdb=" O TYR B 485 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL B 547 " --> pdb=" O PRO B 571 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE B 573 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 577 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 685 through 688 Processing sheet with id= 29, first strand: chain 'B' and resid 800 through 804 removed outlier: 5.853A pdb=" N GLY B 800 " --> pdb=" O ALA B2440 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B2440 " --> pdb=" O GLY B 800 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N THR B 804 " --> pdb=" O GLY B2436 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY B2436 " --> pdb=" O THR B 804 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 951 through 954 removed outlier: 3.680A pdb=" N ARG B 957 " --> pdb=" O TRP B 954 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 972 through 976 removed outlier: 4.642A pdb=" N THR B 994 " --> pdb=" O PRO B 981 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA B 983 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 990 " --> pdb=" O HIS B 985 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 998 " --> pdb=" O HIS B 995 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 999 " --> pdb=" O PHE B1014 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 1060 through 1067 Processing sheet with id= 33, first strand: chain 'B' and resid 1127 through 1130 removed outlier: 6.682A pdb=" N ARG B1185 " --> pdb=" O LEU B1130 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B1131 " --> pdb=" O ARG B1185 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET B1331 " --> pdb=" O ALA B1323 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B1323 " --> pdb=" O MET B1331 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B1337 " --> pdb=" O GLU B1317 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU B1317 " --> pdb=" O LEU B1337 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA B1339 " --> pdb=" O GLY B1315 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLY B1315 " --> pdb=" O ALA B1339 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP B1320 " --> pdb=" O ARG B1309 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG B1309 " --> pdb=" O ASP B1320 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA B1322 " --> pdb=" O VAL B1307 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL B1307 " --> pdb=" O ALA B1322 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 1396 through 1399 removed outlier: 4.692A pdb=" N VAL B1402 " --> pdb=" O ALA B1399 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 1524 through 1527 removed outlier: 6.899A pdb=" N ALA B1537 " --> pdb=" O VAL B1527 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER B1534 " --> pdb=" O PRO B1499 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B1494 " --> pdb=" O VAL B1568 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N SER B1564 " --> pdb=" O ARG B1498 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 1724 through 1728 Processing sheet with id= 37, first strand: chain 'B' and resid 2047 through 2051 removed outlier: 4.095A pdb=" N LEU B2187 " --> pdb=" O PHE B2050 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B2157 " --> pdb=" O GLU B2131 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B2134 " --> pdb=" O LEU B2230 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 2212 through 2215 removed outlier: 4.089A pdb=" N GLN B2218 " --> pdb=" O LEU B2215 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 2282 through 2288 removed outlier: 3.980A pdb=" N ILE B2396 " --> pdb=" O LEU B2338 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY B2344 " --> pdb=" O LEU B2400 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 2471 through 2476 removed outlier: 3.528A pdb=" N GLY B2471 " --> pdb=" O LEU B2827 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B2827 " --> pdb=" O GLY B2471 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B2822 " --> pdb=" O ASP B2774 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 2594 through 2600 Processing sheet with id= 42, first strand: chain 'B' and resid 2847 through 2853 removed outlier: 4.323A pdb=" N PHE B2847 " --> pdb=" O ALA B3013 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP B2853 " --> pdb=" O HIS B3007 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N HIS B3007 " --> pdb=" O ASP B2853 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE B3005 " --> pdb=" O GLY B3006 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B3008 " --> pdb=" O LEU B3003 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU B3003 " --> pdb=" O VAL B3008 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY B3010 " --> pdb=" O THR B3001 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR B3001 " --> pdb=" O GLY B3010 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B3012 " --> pdb=" O MET B2999 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N MET B2999 " --> pdb=" O VAL B3012 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B3014 " --> pdb=" O ALA B2997 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA B2997 " --> pdb=" O LEU B3014 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B2894 " --> pdb=" O ALA B2997 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B3001 " --> pdb=" O SER B2896 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS B2898 " --> pdb=" O THR B3001 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B3003 " --> pdb=" O HIS B2898 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA B2893 " --> pdb=" O PRO B2927 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 2960 through 2963 removed outlier: 6.665A pdb=" N ASP B2985 " --> pdb=" O PRO B2963 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'B' and resid 1163 through 1171 Processing sheet with id= 45, first strand: chain 'B' and resid 1220 through 1227 removed outlier: 3.567A pdb=" N ARG B1220 " --> pdb=" O VAL B1307 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP B1301 " --> pdb=" O ALA B1226 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'B' and resid 1342 through 1346 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'C' and resid 153 through 157 removed outlier: 4.027A pdb=" N ALA C 154 " --> pdb=" O TYR C 44 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLY C 49 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY C 374 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY C 355 " --> pdb=" O ALA C 378 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 245 through 249 removed outlier: 5.295A pdb=" N MET C 207 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 406 through 409 Processing sheet with id= 50, first strand: chain 'C' and resid 455 through 459 removed outlier: 3.526A pdb=" N GLY C 459 " --> pdb=" O ASN C 488 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY C 519 " --> pdb=" O TYR C 485 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL C 547 " --> pdb=" O PRO C 571 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE C 573 " --> pdb=" O VAL C 547 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 577 " --> pdb=" O PRO C 551 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 685 through 688 Processing sheet with id= 52, first strand: chain 'C' and resid 800 through 804 removed outlier: 5.853A pdb=" N GLY C 800 " --> pdb=" O ALA C2440 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C2440 " --> pdb=" O GLY C 800 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N THR C 804 " --> pdb=" O GLY C2436 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY C2436 " --> pdb=" O THR C 804 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 951 through 954 removed outlier: 3.680A pdb=" N ARG C 957 " --> pdb=" O TRP C 954 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 972 through 976 removed outlier: 4.643A pdb=" N THR C 994 " --> pdb=" O PRO C 981 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA C 983 " --> pdb=" O LEU C 992 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 990 " --> pdb=" O HIS C 985 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP C 998 " --> pdb=" O HIS C 995 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 999 " --> pdb=" O PHE C1014 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 1060 through 1067 Processing sheet with id= 56, first strand: chain 'C' and resid 1127 through 1130 removed outlier: 6.681A pdb=" N ARG C1185 " --> pdb=" O LEU C1130 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C1131 " --> pdb=" O ARG C1185 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET C1331 " --> pdb=" O ALA C1323 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C1323 " --> pdb=" O MET C1331 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C1337 " --> pdb=" O GLU C1317 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU C1317 " --> pdb=" O LEU C1337 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ALA C1339 " --> pdb=" O GLY C1315 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLY C1315 " --> pdb=" O ALA C1339 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP C1320 " --> pdb=" O ARG C1309 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARG C1309 " --> pdb=" O ASP C1320 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA C1322 " --> pdb=" O VAL C1307 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL C1307 " --> pdb=" O ALA C1322 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 1396 through 1399 removed outlier: 4.691A pdb=" N VAL C1402 " --> pdb=" O ALA C1399 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 1524 through 1527 removed outlier: 6.899A pdb=" N ALA C1537 " --> pdb=" O VAL C1527 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER C1534 " --> pdb=" O PRO C1499 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU C1494 " --> pdb=" O VAL C1568 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER C1564 " --> pdb=" O ARG C1498 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 1724 through 1728 Processing sheet with id= 60, first strand: chain 'C' and resid 2047 through 2051 removed outlier: 4.095A pdb=" N LEU C2187 " --> pdb=" O PHE C2050 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C2157 " --> pdb=" O GLU C2131 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C2134 " --> pdb=" O LEU C2230 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'C' and resid 2212 through 2215 removed outlier: 4.090A pdb=" N GLN C2218 " --> pdb=" O LEU C2215 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 2282 through 2288 removed outlier: 3.980A pdb=" N ILE C2396 " --> pdb=" O LEU C2338 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY C2344 " --> pdb=" O LEU C2400 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'C' and resid 2471 through 2476 removed outlier: 3.528A pdb=" N GLY C2471 " --> pdb=" O LEU C2827 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU C2827 " --> pdb=" O GLY C2471 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C2822 " --> pdb=" O ASP C2774 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'C' and resid 2594 through 2600 Processing sheet with id= 65, first strand: chain 'C' and resid 2847 through 2853 removed outlier: 4.324A pdb=" N PHE C2847 " --> pdb=" O ALA C3013 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP C2853 " --> pdb=" O HIS C3007 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N HIS C3007 " --> pdb=" O ASP C2853 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE C3005 " --> pdb=" O GLY C3006 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C3008 " --> pdb=" O LEU C3003 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU C3003 " --> pdb=" O VAL C3008 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY C3010 " --> pdb=" O THR C3001 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR C3001 " --> pdb=" O GLY C3010 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL C3012 " --> pdb=" O MET C2999 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET C2999 " --> pdb=" O VAL C3012 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU C3014 " --> pdb=" O ALA C2997 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA C2997 " --> pdb=" O LEU C3014 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C2894 " --> pdb=" O ALA C2997 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C3001 " --> pdb=" O SER C2896 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS C2898 " --> pdb=" O THR C3001 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU C3003 " --> pdb=" O HIS C2898 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA C2893 " --> pdb=" O PRO C2927 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'C' and resid 2960 through 2963 removed outlier: 6.666A pdb=" N ASP C2985 " --> pdb=" O PRO C2963 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'C' and resid 1163 through 1171 Processing sheet with id= 68, first strand: chain 'C' and resid 1220 through 1227 removed outlier: 3.567A pdb=" N ARG C1220 " --> pdb=" O VAL C1307 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP C1301 " --> pdb=" O ALA C1226 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'C' and resid 1342 through 1346 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 'D' and resid 153 through 157 removed outlier: 4.026A pdb=" N ALA D 154 " --> pdb=" O TYR D 44 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLY D 49 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY D 374 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY D 355 " --> pdb=" O ALA D 378 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 245 through 249 removed outlier: 5.296A pdb=" N MET D 207 " --> pdb=" O VAL D 290 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 406 through 409 Processing sheet with id= 73, first strand: chain 'D' and resid 455 through 459 removed outlier: 3.526A pdb=" N GLY D 459 " --> pdb=" O ASN D 488 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY D 519 " --> pdb=" O TYR D 485 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL D 547 " --> pdb=" O PRO D 571 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE D 573 " --> pdb=" O VAL D 547 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU D 577 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 685 through 688 Processing sheet with id= 75, first strand: chain 'D' and resid 800 through 804 removed outlier: 5.854A pdb=" N GLY D 800 " --> pdb=" O ALA D2440 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D2440 " --> pdb=" O GLY D 800 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N THR D 804 " --> pdb=" O GLY D2436 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY D2436 " --> pdb=" O THR D 804 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 951 through 954 removed outlier: 3.680A pdb=" N ARG D 957 " --> pdb=" O TRP D 954 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'D' and resid 972 through 976 removed outlier: 4.643A pdb=" N THR D 994 " --> pdb=" O PRO D 981 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA D 983 " --> pdb=" O LEU D 992 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA D 990 " --> pdb=" O HIS D 985 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP D 998 " --> pdb=" O HIS D 995 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 999 " --> pdb=" O PHE D1014 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 1060 through 1067 Processing sheet with id= 79, first strand: chain 'D' and resid 1127 through 1130 removed outlier: 6.682A pdb=" N ARG D1185 " --> pdb=" O LEU D1130 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D1131 " --> pdb=" O ARG D1185 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET D1331 " --> pdb=" O ALA D1323 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D1323 " --> pdb=" O MET D1331 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D1337 " --> pdb=" O GLU D1317 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU D1317 " --> pdb=" O LEU D1337 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA D1339 " --> pdb=" O GLY D1315 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLY D1315 " --> pdb=" O ALA D1339 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP D1320 " --> pdb=" O ARG D1309 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG D1309 " --> pdb=" O ASP D1320 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA D1322 " --> pdb=" O VAL D1307 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL D1307 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 1396 through 1399 removed outlier: 4.691A pdb=" N VAL D1402 " --> pdb=" O ALA D1399 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'D' and resid 1524 through 1527 removed outlier: 6.900A pdb=" N ALA D1537 " --> pdb=" O VAL D1527 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER D1534 " --> pdb=" O PRO D1499 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU D1494 " --> pdb=" O VAL D1568 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N SER D1564 " --> pdb=" O ARG D1498 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'D' and resid 1724 through 1728 Processing sheet with id= 83, first strand: chain 'D' and resid 2047 through 2051 removed outlier: 4.094A pdb=" N LEU D2187 " --> pdb=" O PHE D2050 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR D2157 " --> pdb=" O GLU D2131 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL D2134 " --> pdb=" O LEU D2230 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'D' and resid 2212 through 2215 removed outlier: 4.089A pdb=" N GLN D2218 " --> pdb=" O LEU D2215 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'D' and resid 2282 through 2288 removed outlier: 3.980A pdb=" N ILE D2396 " --> pdb=" O LEU D2338 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY D2344 " --> pdb=" O LEU D2400 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'D' and resid 2471 through 2476 removed outlier: 3.527A pdb=" N GLY D2471 " --> pdb=" O LEU D2827 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU D2827 " --> pdb=" O GLY D2471 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D2822 " --> pdb=" O ASP D2774 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'D' and resid 2594 through 2600 Processing sheet with id= 88, first strand: chain 'D' and resid 2847 through 2853 removed outlier: 4.323A pdb=" N PHE D2847 " --> pdb=" O ALA D3013 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP D2853 " --> pdb=" O HIS D3007 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N HIS D3007 " --> pdb=" O ASP D2853 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE D3005 " --> pdb=" O GLY D3006 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL D3008 " --> pdb=" O LEU D3003 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU D3003 " --> pdb=" O VAL D3008 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY D3010 " --> pdb=" O THR D3001 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR D3001 " --> pdb=" O GLY D3010 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D3012 " --> pdb=" O MET D2999 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET D2999 " --> pdb=" O VAL D3012 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU D3014 " --> pdb=" O ALA D2997 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA D2997 " --> pdb=" O LEU D3014 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL D2894 " --> pdb=" O ALA D2997 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR D3001 " --> pdb=" O SER D2896 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS D2898 " --> pdb=" O THR D3001 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU D3003 " --> pdb=" O HIS D2898 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA D2893 " --> pdb=" O PRO D2927 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'D' and resid 2960 through 2963 removed outlier: 6.665A pdb=" N ASP D2985 " --> pdb=" O PRO D2963 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'D' and resid 1163 through 1171 Processing sheet with id= 91, first strand: chain 'D' and resid 1220 through 1227 removed outlier: 3.568A pdb=" N ARG D1220 " --> pdb=" O VAL D1307 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP D1301 " --> pdb=" O ALA D1226 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'D' and resid 1342 through 1346 No H-bonds generated for sheet with id= 92 Processing sheet with id= 93, first strand: chain 'E' and resid 153 through 157 removed outlier: 4.027A pdb=" N ALA E 154 " --> pdb=" O TYR E 44 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLY E 49 " --> pdb=" O LEU E 354 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY E 374 " --> pdb=" O ARG E 349 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY E 355 " --> pdb=" O ALA E 378 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'E' and resid 245 through 249 removed outlier: 5.296A pdb=" N MET E 207 " --> pdb=" O VAL E 290 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'E' and resid 406 through 409 Processing sheet with id= 96, first strand: chain 'E' and resid 455 through 459 removed outlier: 3.526A pdb=" N GLY E 459 " --> pdb=" O ASN E 488 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY E 519 " --> pdb=" O TYR E 485 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL E 547 " --> pdb=" O PRO E 571 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE E 573 " --> pdb=" O VAL E 547 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU E 577 " --> pdb=" O PRO E 551 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'E' and resid 685 through 688 Processing sheet with id= 98, first strand: chain 'E' and resid 800 through 804 removed outlier: 5.853A pdb=" N GLY E 800 " --> pdb=" O ALA E2440 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E2440 " --> pdb=" O GLY E 800 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR E 804 " --> pdb=" O GLY E2436 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY E2436 " --> pdb=" O THR E 804 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'E' and resid 951 through 954 removed outlier: 3.680A pdb=" N ARG E 957 " --> pdb=" O TRP E 954 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'E' and resid 972 through 976 removed outlier: 4.642A pdb=" N THR E 994 " --> pdb=" O PRO E 981 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA E 983 " --> pdb=" O LEU E 992 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 990 " --> pdb=" O HIS E 985 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP E 998 " --> pdb=" O HIS E 995 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E 999 " --> pdb=" O PHE E1014 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'E' and resid 1060 through 1067 Processing sheet with id=102, first strand: chain 'E' and resid 1127 through 1130 removed outlier: 6.682A pdb=" N ARG E1185 " --> pdb=" O LEU E1130 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP E1131 " --> pdb=" O ARG E1185 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET E1331 " --> pdb=" O ALA E1323 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA E1323 " --> pdb=" O MET E1331 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU E1337 " --> pdb=" O GLU E1317 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU E1317 " --> pdb=" O LEU E1337 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA E1339 " --> pdb=" O GLY E1315 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N GLY E1315 " --> pdb=" O ALA E1339 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP E1320 " --> pdb=" O ARG E1309 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG E1309 " --> pdb=" O ASP E1320 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA E1322 " --> pdb=" O VAL E1307 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL E1307 " --> pdb=" O ALA E1322 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'E' and resid 1396 through 1399 removed outlier: 4.691A pdb=" N VAL E1402 " --> pdb=" O ALA E1399 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'E' and resid 1524 through 1527 removed outlier: 6.900A pdb=" N ALA E1537 " --> pdb=" O VAL E1527 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER E1534 " --> pdb=" O PRO E1499 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU E1494 " --> pdb=" O VAL E1568 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N SER E1564 " --> pdb=" O ARG E1498 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'E' and resid 1724 through 1728 Processing sheet with id=106, first strand: chain 'E' and resid 2047 through 2051 removed outlier: 4.095A pdb=" N LEU E2187 " --> pdb=" O PHE E2050 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR E2157 " --> pdb=" O GLU E2131 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL E2134 " --> pdb=" O LEU E2230 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'E' and resid 2212 through 2215 removed outlier: 4.090A pdb=" N GLN E2218 " --> pdb=" O LEU E2215 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'E' and resid 2282 through 2288 removed outlier: 3.980A pdb=" N ILE E2396 " --> pdb=" O LEU E2338 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY E2344 " --> pdb=" O LEU E2400 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'E' and resid 2471 through 2476 removed outlier: 3.527A pdb=" N GLY E2471 " --> pdb=" O LEU E2827 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU E2827 " --> pdb=" O GLY E2471 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY E2822 " --> pdb=" O ASP E2774 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'E' and resid 2594 through 2600 Processing sheet with id=111, first strand: chain 'E' and resid 2847 through 2853 removed outlier: 4.324A pdb=" N PHE E2847 " --> pdb=" O ALA E3013 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP E2853 " --> pdb=" O HIS E3007 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N HIS E3007 " --> pdb=" O ASP E2853 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE E3005 " --> pdb=" O GLY E3006 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL E3008 " --> pdb=" O LEU E3003 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU E3003 " --> pdb=" O VAL E3008 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY E3010 " --> pdb=" O THR E3001 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR E3001 " --> pdb=" O GLY E3010 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E3012 " --> pdb=" O MET E2999 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET E2999 " --> pdb=" O VAL E3012 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU E3014 " --> pdb=" O ALA E2997 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA E2997 " --> pdb=" O LEU E3014 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL E2894 " --> pdb=" O ALA E2997 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR E3001 " --> pdb=" O SER E2896 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS E2898 " --> pdb=" O THR E3001 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU E3003 " --> pdb=" O HIS E2898 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA E2893 " --> pdb=" O PRO E2927 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'E' and resid 2960 through 2963 removed outlier: 6.665A pdb=" N ASP E2985 " --> pdb=" O PRO E2963 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'E' and resid 1163 through 1171 Processing sheet with id=114, first strand: chain 'E' and resid 1220 through 1227 removed outlier: 3.566A pdb=" N ARG E1220 " --> pdb=" O VAL E1307 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP E1301 " --> pdb=" O ALA E1226 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'E' and resid 1342 through 1346 No H-bonds generated for sheet with id=115 Processing sheet with id=116, first strand: chain 'F' and resid 153 through 157 removed outlier: 4.027A pdb=" N ALA F 154 " --> pdb=" O TYR F 44 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLY F 49 " --> pdb=" O LEU F 354 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY F 374 " --> pdb=" O ARG F 349 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY F 355 " --> pdb=" O ALA F 378 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'F' and resid 245 through 249 removed outlier: 5.296A pdb=" N MET F 207 " --> pdb=" O VAL F 290 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'F' and resid 406 through 409 Processing sheet with id=119, first strand: chain 'F' and resid 455 through 459 removed outlier: 3.526A pdb=" N GLY F 459 " --> pdb=" O ASN F 488 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY F 519 " --> pdb=" O TYR F 485 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL F 547 " --> pdb=" O PRO F 571 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE F 573 " --> pdb=" O VAL F 547 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU F 577 " --> pdb=" O PRO F 551 " (cutoff:3.500A) Processing sheet with id=120, first strand: chain 'F' and resid 685 through 688 Processing sheet with id=121, first strand: chain 'F' and resid 800 through 804 removed outlier: 5.853A pdb=" N GLY F 800 " --> pdb=" O ALA F2440 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA F2440 " --> pdb=" O GLY F 800 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR F 804 " --> pdb=" O GLY F2436 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY F2436 " --> pdb=" O THR F 804 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'F' and resid 951 through 954 removed outlier: 3.679A pdb=" N ARG F 957 " --> pdb=" O TRP F 954 " (cutoff:3.500A) Processing sheet with id=123, first strand: chain 'F' and resid 972 through 976 removed outlier: 4.643A pdb=" N THR F 994 " --> pdb=" O PRO F 981 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA F 983 " --> pdb=" O LEU F 992 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA F 990 " --> pdb=" O HIS F 985 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP F 998 " --> pdb=" O HIS F 995 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL F 999 " --> pdb=" O PHE F1014 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'F' and resid 1060 through 1067 Processing sheet with id=125, first strand: chain 'F' and resid 1127 through 1130 removed outlier: 6.682A pdb=" N ARG F1185 " --> pdb=" O LEU F1130 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP F1131 " --> pdb=" O ARG F1185 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET F1331 " --> pdb=" O ALA F1323 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F1323 " --> pdb=" O MET F1331 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F1337 " --> pdb=" O GLU F1317 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU F1317 " --> pdb=" O LEU F1337 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA F1339 " --> pdb=" O GLY F1315 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLY F1315 " --> pdb=" O ALA F1339 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP F1320 " --> pdb=" O ARG F1309 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG F1309 " --> pdb=" O ASP F1320 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA F1322 " --> pdb=" O VAL F1307 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL F1307 " --> pdb=" O ALA F1322 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 'F' and resid 1396 through 1399 removed outlier: 4.692A pdb=" N VAL F1402 " --> pdb=" O ALA F1399 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 'F' and resid 1524 through 1527 removed outlier: 6.900A pdb=" N ALA F1537 " --> pdb=" O VAL F1527 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER F1534 " --> pdb=" O PRO F1499 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU F1494 " --> pdb=" O VAL F1568 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N SER F1564 " --> pdb=" O ARG F1498 " (cutoff:3.500A) Processing sheet with id=128, first strand: chain 'F' and resid 1724 through 1728 Processing sheet with id=129, first strand: chain 'F' and resid 2047 through 2051 removed outlier: 4.095A pdb=" N LEU F2187 " --> pdb=" O PHE F2050 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR F2157 " --> pdb=" O GLU F2131 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL F2134 " --> pdb=" O LEU F2230 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'F' and resid 2212 through 2215 removed outlier: 4.089A pdb=" N GLN F2218 " --> pdb=" O LEU F2215 " (cutoff:3.500A) Processing sheet with id=131, first strand: chain 'F' and resid 2282 through 2288 removed outlier: 3.979A pdb=" N ILE F2396 " --> pdb=" O LEU F2338 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY F2344 " --> pdb=" O LEU F2400 " (cutoff:3.500A) Processing sheet with id=132, first strand: chain 'F' and resid 2471 through 2476 removed outlier: 3.528A pdb=" N GLY F2471 " --> pdb=" O LEU F2827 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU F2827 " --> pdb=" O GLY F2471 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY F2822 " --> pdb=" O ASP F2774 " (cutoff:3.500A) Processing sheet with id=133, first strand: chain 'F' and resid 2594 through 2600 Processing sheet with id=134, first strand: chain 'F' and resid 2847 through 2853 removed outlier: 4.324A pdb=" N PHE F2847 " --> pdb=" O ALA F3013 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP F2853 " --> pdb=" O HIS F3007 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N HIS F3007 " --> pdb=" O ASP F2853 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE F3005 " --> pdb=" O GLY F3006 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL F3008 " --> pdb=" O LEU F3003 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU F3003 " --> pdb=" O VAL F3008 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY F3010 " --> pdb=" O THR F3001 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR F3001 " --> pdb=" O GLY F3010 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL F3012 " --> pdb=" O MET F2999 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET F2999 " --> pdb=" O VAL F3012 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU F3014 " --> pdb=" O ALA F2997 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA F2997 " --> pdb=" O LEU F3014 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL F2894 " --> pdb=" O ALA F2997 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR F3001 " --> pdb=" O SER F2896 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS F2898 " --> pdb=" O THR F3001 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU F3003 " --> pdb=" O HIS F2898 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ALA F2893 " --> pdb=" O PRO F2927 " (cutoff:3.500A) Processing sheet with id=135, first strand: chain 'F' and resid 2960 through 2963 removed outlier: 6.665A pdb=" N ASP F2985 " --> pdb=" O PRO F2963 " (cutoff:3.500A) Processing sheet with id=136, first strand: chain 'F' and resid 1163 through 1171 Processing sheet with id=137, first strand: chain 'F' and resid 1220 through 1227 removed outlier: 3.567A pdb=" N ARG F1220 " --> pdb=" O VAL F1307 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP F1301 " --> pdb=" O ALA F1226 " (cutoff:3.500A) Processing sheet with id=138, first strand: chain 'F' and resid 1342 through 1346 No H-bonds generated for sheet with id=138 6210 hydrogen bonds defined for protein. 18414 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: 94.72 Time building geometry restraints manager: 40.38 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: 34673 1.33 - 1.45: 21126 1.45 - 1.57: 71029 1.57 - 1.69: 6 1.69 - 1.81: 702 Bond restraints: 127536 Sorted by residual: bond pdb=" CG LEU B2762 " pdb=" CD2 LEU B2762 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.18e+00 bond pdb=" CG LEU F2762 " pdb=" CD2 LEU F2762 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.18e+00 bond pdb=" CG LEU C2762 " pdb=" CD2 LEU C2762 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.14e+00 bond pdb=" CG LEU D2762 " pdb=" CD2 LEU D2762 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.10e+00 bond pdb=" CG LEU E2762 " pdb=" CD2 LEU E2762 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.09e+00 ... (remaining 127531 not shown) Histogram of bond angle deviations from ideal: 97.54 - 105.08: 3118 105.08 - 112.62: 66566 112.62 - 120.16: 52010 120.16 - 127.70: 50775 127.70 - 135.25: 1441 Bond angle restraints: 173910 Sorted by residual: angle pdb=" C ARG C2182 " pdb=" N TYR C2183 " pdb=" CA TYR C2183 " ideal model delta sigma weight residual 121.19 128.98 -7.79 1.59e+00 3.96e-01 2.40e+01 angle pdb=" C ARG A2182 " pdb=" N TYR A2183 " pdb=" CA TYR A2183 " ideal model delta sigma weight residual 121.19 128.97 -7.78 1.59e+00 3.96e-01 2.39e+01 angle pdb=" C ARG E2182 " pdb=" N TYR E2183 " pdb=" CA TYR E2183 " ideal model delta sigma weight residual 121.19 128.96 -7.77 1.59e+00 3.96e-01 2.39e+01 angle pdb=" C ARG B2182 " pdb=" N TYR B2183 " pdb=" CA TYR B2183 " ideal model delta sigma weight residual 121.19 128.95 -7.76 1.59e+00 3.96e-01 2.38e+01 angle pdb=" C ARG D2182 " pdb=" N TYR D2183 " pdb=" CA TYR D2183 " ideal model delta sigma weight residual 121.19 128.94 -7.75 1.59e+00 3.96e-01 2.37e+01 ... (remaining 173905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.92: 71161 14.92 - 29.85: 3826 29.85 - 44.77: 997 44.77 - 59.70: 66 59.70 - 74.62: 42 Dihedral angle restraints: 76092 sinusoidal: 29040 harmonic: 47052 Sorted by residual: dihedral pdb=" CA THR C 848 " pdb=" C THR C 848 " pdb=" N LEU C 849 " pdb=" CA LEU C 849 " ideal model delta harmonic sigma weight residual 180.00 133.85 46.15 0 5.00e+00 4.00e-02 8.52e+01 dihedral pdb=" CA THR F 848 " pdb=" C THR F 848 " pdb=" N LEU F 849 " pdb=" CA LEU F 849 " ideal model delta harmonic sigma weight residual 180.00 133.85 46.15 0 5.00e+00 4.00e-02 8.52e+01 dihedral pdb=" CA THR B 848 " pdb=" C THR B 848 " pdb=" N LEU B 849 " pdb=" CA LEU B 849 " ideal model delta harmonic sigma weight residual 180.00 133.86 46.14 0 5.00e+00 4.00e-02 8.52e+01 ... (remaining 76089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 15382 0.070 - 0.140: 3938 0.140 - 0.210: 571 0.210 - 0.280: 95 0.280 - 0.350: 30 Chirality restraints: 20016 Sorted by residual: chirality pdb=" CB VAL A1093 " pdb=" CA VAL A1093 " pdb=" CG1 VAL A1093 " pdb=" CG2 VAL A1093 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB VAL C1093 " pdb=" CA VAL C1093 " pdb=" CG1 VAL C1093 " pdb=" CG2 VAL C1093 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB VAL F1093 " pdb=" CA VAL F1093 " pdb=" CG1 VAL F1093 " pdb=" CG2 VAL F1093 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 20013 not shown) Planarity restraints: 22932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B2741 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO B2742 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B2742 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B2742 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F2741 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO F2742 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO F2742 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F2742 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A2741 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO A2742 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A2742 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A2742 " 0.039 5.00e-02 4.00e+02 ... (remaining 22929 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 26844 2.78 - 3.31: 114614 3.31 - 3.84: 205631 3.84 - 4.37: 226210 4.37 - 4.90: 398237 Nonbonded interactions: 971536 Sorted by model distance: nonbonded pdb=" OE2 GLU E1451 " pdb=" OH TYR E1608 " model vdw 2.247 2.440 nonbonded pdb=" OE2 GLU B1451 " pdb=" OH TYR B1608 " model vdw 2.247 2.440 nonbonded pdb=" OE2 GLU A1451 " pdb=" OH TYR A1608 " model vdw 2.248 2.440 nonbonded pdb=" OE2 GLU C1451 " pdb=" OH TYR C1608 " model vdw 2.248 2.440 nonbonded pdb=" OE2 GLU D1451 " pdb=" OH TYR D1608 " model vdw 2.248 2.440 ... (remaining 971531 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' selection = chain 'F' } 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 17.010 Check model and map are aligned: 1.310 Set scattering table: 0.840 Process input model: 317.740 Find NCS groups from input model: 7.030 Set up NCS constraints: 0.700 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 349.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 127536 Z= 0.519 Angle : 1.072 13.710 173910 Z= 0.578 Chirality : 0.064 0.350 20016 Planarity : 0.008 0.071 22932 Dihedral : 10.270 74.621 45876 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.03 % Allowed : 5.57 % Favored : 93.40 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.24 % 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: -4.03 (0.05), residues: 16572 helix: -2.43 (0.04), residues: 7272 sheet: -2.02 (0.10), residues: 2112 loop : -3.06 (0.06), residues: 7188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP F 749 HIS 0.021 0.003 HIS D2727 PHE 0.038 0.003 PHE C1983 TYR 0.030 0.003 TYR C2128 ARG 0.009 0.001 ARG F1191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1940 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1808 time to evaluate : 8.864 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: 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 475 MET cc_start: 0.9195 (mmm) cc_final: 0.8803 (mmm) REVERT: A 710 ASP cc_start: 0.7504 (m-30) cc_final: 0.7125 (m-30) REVERT: A 888 ILE cc_start: 0.8983 (pt) cc_final: 0.8761 (pt) REVERT: A 1356 MET cc_start: 0.7539 (mtm) cc_final: 0.7289 (mtp) REVERT: A 1395 THR cc_start: 0.8653 (m) cc_final: 0.8414 (p) REVERT: A 2209 THR cc_start: 0.8708 (p) cc_final: 0.8171 (p) REVERT: A 2251 GLU cc_start: 0.8685 (pp20) cc_final: 0.8258 (pm20) REVERT: A 2411 MET cc_start: 0.5783 (ttp) cc_final: 0.5253 (mtt) REVERT: B 475 MET cc_start: 0.8785 (mmm) cc_final: 0.8525 (mmm) REVERT: B 1498 ARG cc_start: 0.8650 (ttm170) cc_final: 0.8036 (ttm-80) REVERT: B 1654 MET cc_start: 0.9325 (ttp) cc_final: 0.9009 (ptm) REVERT: B 2411 MET cc_start: 0.5820 (ttp) cc_final: 0.5246 (mtt) REVERT: B 2438 ILE cc_start: 0.8891 (tp) cc_final: 0.8615 (pt) REVERT: C 475 MET cc_start: 0.8958 (mmm) cc_final: 0.8640 (mmm) REVERT: C 1161 MET cc_start: 0.8353 (ppp) cc_final: 0.7858 (ppp) REVERT: C 1498 ARG cc_start: 0.8777 (ttm170) cc_final: 0.8302 (ttp80) REVERT: C 1640 LEU cc_start: 0.9570 (tm) cc_final: 0.9327 (tm) REVERT: C 1654 MET cc_start: 0.9230 (ttp) cc_final: 0.8920 (ptm) REVERT: C 2254 MET cc_start: 0.9053 (tmt) cc_final: 0.8641 (tmm) REVERT: C 2411 MET cc_start: 0.6422 (ttp) cc_final: 0.5812 (mtt) REVERT: C 2692 MET cc_start: 0.4602 (tmt) cc_final: 0.3864 (tmt) REVERT: D 214 ASP cc_start: 0.8042 (t0) cc_final: 0.7821 (t0) REVERT: D 1037 MET cc_start: 0.8406 (mmt) cc_final: 0.7971 (mmm) REVERT: D 1654 MET cc_start: 0.9372 (ttp) cc_final: 0.8939 (ptm) REVERT: D 1727 ASN cc_start: 0.8660 (t0) cc_final: 0.8292 (t0) REVERT: D 2201 ASP cc_start: 0.7868 (m-30) cc_final: 0.7415 (m-30) REVERT: D 2253 GLU cc_start: 0.8942 (pp20) cc_final: 0.8707 (pp20) REVERT: D 2254 MET cc_start: 0.9202 (tmt) cc_final: 0.8990 (tpp) REVERT: D 2411 MET cc_start: 0.4613 (ttp) cc_final: 0.4265 (mtt) REVERT: D 2438 ILE cc_start: 0.8705 (tp) cc_final: 0.8477 (pt) REVERT: D 2586 PHE cc_start: 0.9175 (t80) cc_final: 0.8922 (t80) REVERT: D 2692 MET cc_start: 0.4341 (tmt) cc_final: 0.3896 (tmt) REVERT: E 90 LEU cc_start: 0.9090 (tp) cc_final: 0.8879 (tt) REVERT: E 475 MET cc_start: 0.8971 (mmm) cc_final: 0.8615 (mmm) REVERT: E 585 HIS cc_start: 0.7356 (t-170) cc_final: 0.6894 (t-170) REVERT: E 710 ASP cc_start: 0.7374 (m-30) cc_final: 0.7070 (m-30) REVERT: E 1037 MET cc_start: 0.8483 (mmt) cc_final: 0.8279 (mmt) REVERT: E 1535 GLN cc_start: 0.8017 (tp40) cc_final: 0.7575 (tp-100) REVERT: E 1654 MET cc_start: 0.9442 (ttp) cc_final: 0.8999 (ptm) REVERT: E 1667 PHE cc_start: 0.8186 (t80) cc_final: 0.7976 (t80) REVERT: E 1727 ASN cc_start: 0.8746 (t0) cc_final: 0.8342 (t0) REVERT: E 2201 ASP cc_start: 0.7933 (m-30) cc_final: 0.7542 (m-30) REVERT: E 2411 MET cc_start: 0.5147 (ttp) cc_final: 0.4753 (mtt) REVERT: E 2586 PHE cc_start: 0.9249 (t80) cc_final: 0.9049 (t80) REVERT: F 214 ASP cc_start: 0.7857 (t0) cc_final: 0.7656 (t0) REVERT: F 475 MET cc_start: 0.8825 (mmm) cc_final: 0.8581 (mmm) REVERT: F 710 ASP cc_start: 0.7938 (m-30) cc_final: 0.7542 (m-30) REVERT: F 1493 ARG cc_start: 0.6944 (mpt180) cc_final: 0.6739 (mmt-90) REVERT: F 1498 ARG cc_start: 0.8738 (ttm170) cc_final: 0.8195 (ttp80) REVERT: F 1553 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8349 (mm-30) REVERT: F 1587 PHE cc_start: 0.8136 (t80) cc_final: 0.7634 (t80) REVERT: F 1591 LEU cc_start: 0.8993 (tp) cc_final: 0.8572 (mt) REVERT: F 1625 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8684 (tp-100) REVERT: F 1654 MET cc_start: 0.9260 (ttp) cc_final: 0.8922 (ptm) REVERT: F 2254 MET cc_start: 0.9042 (tmt) cc_final: 0.8694 (tmm) REVERT: F 2411 MET cc_start: 0.5431 (ttp) cc_final: 0.4912 (mtt) REVERT: F 2438 ILE cc_start: 0.8838 (tp) cc_final: 0.8607 (pt) REVERT: F 2586 PHE cc_start: 0.9355 (t80) cc_final: 0.8993 (t80) outliers start: 132 outliers final: 30 residues processed: 1921 average time/residue: 1.1227 time to fit residues: 3637.7571 Evaluate side-chains 916 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 886 time to evaluate : 9.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 1986 GLN Chi-restraints excluded: chain B residue 3012 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 3012 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 3012 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 849 LEU Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 1986 GLN Chi-restraints excluded: chain F residue 3012 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1662 random chunks: chunk 1403 optimal weight: 2.9990 chunk 1259 optimal weight: 7.9990 chunk 698 optimal weight: 4.9990 chunk 430 optimal weight: 20.0000 chunk 849 optimal weight: 1.9990 chunk 673 optimal weight: 0.8980 chunk 1302 optimal weight: 5.9990 chunk 504 optimal weight: 9.9990 chunk 792 optimal weight: 0.2980 chunk 969 optimal weight: 3.9990 chunk 1509 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 183 GLN A 254 GLN A 297 HIS A 344 HIS A 486 GLN A1353 HIS A1403 HIS A1406 HIS ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1625 GLN ** A1986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2109 HIS A2180 HIS A2193 ASN A2221 HIS A2606 GLN A2680 HIS A2705 ASN ** A2802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2821 GLN ** A3007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 183 GLN B 254 GLN B 297 HIS B 486 GLN ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1353 HIS B1388 HIS B1403 HIS B1418 GLN B2109 HIS B2180 HIS B2193 ASN ** B2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2606 GLN B2680 HIS B2705 ASN B2821 GLN ** B3007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 HIS C 183 GLN C 254 GLN C 297 HIS C 486 GLN C1279 GLN C1353 HIS C1388 HIS C1403 HIS C1406 HIS ** C1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2109 HIS C2180 HIS C2193 ASN C2221 HIS ** C2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2606 GLN C2680 HIS C2705 ASN C2802 HIS C2821 GLN ** C3007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS D 183 GLN D 254 GLN D 297 HIS D 486 GLN ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN D1353 HIS D1406 HIS ** D1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2012 ASN D2109 HIS D2180 HIS D2193 ASN ** D2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2680 HIS D2705 ASN D2802 HIS D2821 GLN ** D3007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS E 183 GLN E 254 GLN E 297 HIS E 344 HIS E 486 GLN E1279 GLN E1403 HIS E1406 HIS ** E1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1625 GLN ** E1986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2012 ASN E2109 HIS E2180 HIS E2193 ASN E2606 GLN E2680 HIS ** E2730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2821 GLN F 118 HIS F 183 GLN F 254 GLN F 297 HIS F 486 GLN ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1353 HIS F1388 HIS F1403 HIS F1418 GLN F2109 HIS F2180 HIS F2193 ASN ** F2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2606 GLN F2680 HIS F2821 GLN Total number of N/Q/H flips: 101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 127536 Z= 0.239 Angle : 0.676 11.136 173910 Z= 0.349 Chirality : 0.046 0.269 20016 Planarity : 0.006 0.104 22932 Dihedral : 5.948 56.149 18089 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.08 % Allowed : 8.56 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.13 % 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: -2.46 (0.06), residues: 16572 helix: -0.56 (0.06), residues: 7386 sheet: -1.97 (0.10), residues: 2076 loop : -2.67 (0.06), residues: 7110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 749 HIS 0.013 0.001 HIS A1403 PHE 0.045 0.002 PHE B1983 TYR 0.018 0.001 TYR E 261 ARG 0.009 0.001 ARG C3034 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 394 poor density : 998 time to evaluate : 9.946 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: 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 475 MET cc_start: 0.9084 (mmm) cc_final: 0.8882 (mmm) REVERT: A 570 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8469 (mmmt) REVERT: A 684 MET cc_start: 0.8370 (mmm) cc_final: 0.7597 (mmm) REVERT: A 708 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9123 (tm) REVERT: A 710 ASP cc_start: 0.7497 (m-30) cc_final: 0.7100 (m-30) REVERT: A 811 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8067 (pp) REVERT: A 888 ILE cc_start: 0.9129 (pt) cc_final: 0.8927 (pt) REVERT: A 1729 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8424 (mm-30) REVERT: A 2251 GLU cc_start: 0.8849 (pp20) cc_final: 0.8172 (pm20) REVERT: A 2411 MET cc_start: 0.5708 (ttp) cc_final: 0.5135 (mtt) REVERT: A 2650 ILE cc_start: 0.7234 (mp) cc_final: 0.6914 (tp) REVERT: A 2666 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8855 (mm) REVERT: A 2999 MET cc_start: 0.7315 (mmm) cc_final: 0.6938 (mtp) REVERT: B 102 GLN cc_start: 0.8542 (mp10) cc_final: 0.7471 (mp10) REVERT: B 811 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7833 (pp) REVERT: B 1252 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8872 (tp) REVERT: B 1403 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.7103 (p90) REVERT: B 1498 ARG cc_start: 0.8616 (ttm170) cc_final: 0.8109 (ttm-80) REVERT: B 1626 GLU cc_start: 0.9157 (tt0) cc_final: 0.8832 (mt-10) REVERT: B 1654 MET cc_start: 0.9257 (ttp) cc_final: 0.8965 (ptm) REVERT: B 2231 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8697 (tt) REVERT: B 2411 MET cc_start: 0.5823 (ttp) cc_final: 0.5126 (mtt) REVERT: B 2438 ILE cc_start: 0.8918 (tp) cc_final: 0.8514 (pt) REVERT: B 2586 PHE cc_start: 0.9249 (t80) cc_final: 0.9036 (t80) REVERT: B 2646 MET cc_start: 0.8770 (mmm) cc_final: 0.8428 (tpt) REVERT: C 588 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7991 (mm-30) REVERT: C 811 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7415 (pp) REVERT: C 1037 MET cc_start: 0.8789 (mmp) cc_final: 0.8512 (mmp) REVERT: C 1498 ARG cc_start: 0.8664 (ttm170) cc_final: 0.8229 (ttp80) REVERT: C 1654 MET cc_start: 0.9225 (ttp) cc_final: 0.8978 (ptm) REVERT: C 1679 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8739 (tt) REVERT: C 2254 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8798 (tpp) REVERT: C 2411 MET cc_start: 0.6437 (ttp) cc_final: 0.5834 (mtt) REVERT: C 2586 PHE cc_start: 0.9326 (t80) cc_final: 0.9029 (t80) REVERT: D 90 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8948 (mp) REVERT: D 214 ASP cc_start: 0.8028 (t0) cc_final: 0.7790 (t0) REVERT: D 475 MET cc_start: 0.8948 (mmm) cc_final: 0.8705 (mmm) REVERT: D 811 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7994 (pp) REVERT: D 1646 TRP cc_start: 0.8945 (m-10) cc_final: 0.8332 (m-10) REVERT: D 1654 MET cc_start: 0.9376 (ttp) cc_final: 0.9062 (ptm) REVERT: D 1727 ASN cc_start: 0.8603 (t0) cc_final: 0.8400 (t0) REVERT: D 2201 ASP cc_start: 0.7961 (m-30) cc_final: 0.7566 (m-30) REVERT: D 2253 GLU cc_start: 0.8893 (pp20) cc_final: 0.8546 (pp20) REVERT: D 2254 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8890 (tmm) REVERT: D 2411 MET cc_start: 0.4598 (ttp) cc_final: 0.4195 (mtt) REVERT: D 2586 PHE cc_start: 0.9220 (t80) cc_final: 0.8864 (t80) REVERT: E 90 LEU cc_start: 0.9024 (tp) cc_final: 0.8810 (tt) REVERT: E 585 HIS cc_start: 0.7097 (t-170) cc_final: 0.6740 (t-170) REVERT: E 710 ASP cc_start: 0.7479 (m-30) cc_final: 0.7204 (m-30) REVERT: E 1535 GLN cc_start: 0.7839 (tp40) cc_final: 0.7350 (tp-100) REVERT: E 1654 MET cc_start: 0.9440 (ttp) cc_final: 0.9132 (ptm) REVERT: E 1727 ASN cc_start: 0.8743 (t0) cc_final: 0.8510 (t0) REVERT: E 2036 ARG cc_start: 0.8426 (ptm-80) cc_final: 0.8070 (ppt170) REVERT: E 2254 MET cc_start: 0.9355 (tpp) cc_final: 0.9125 (tpp) REVERT: E 2411 MET cc_start: 0.5184 (ttp) cc_final: 0.4794 (mtt) REVERT: E 2586 PHE cc_start: 0.9245 (t80) cc_final: 0.8961 (t80) REVERT: F 102 GLN cc_start: 0.8502 (mp10) cc_final: 0.7507 (mp10) REVERT: F 214 ASP cc_start: 0.7949 (t0) cc_final: 0.7722 (t0) REVERT: F 811 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7829 (pp) REVERT: F 1403 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.7183 (p90) REVERT: F 1498 ARG cc_start: 0.8707 (ttm170) cc_final: 0.8233 (ttp80) REVERT: F 1654 MET cc_start: 0.9324 (ttp) cc_final: 0.8960 (ptm) REVERT: F 1693 ARG cc_start: 0.8903 (mtm-85) cc_final: 0.8632 (ttm-80) REVERT: F 2254 MET cc_start: 0.9113 (tmt) cc_final: 0.8759 (tmm) REVERT: F 2411 MET cc_start: 0.5665 (ttp) cc_final: 0.5098 (mtt) REVERT: F 2438 ILE cc_start: 0.8872 (tp) cc_final: 0.8510 (pt) REVERT: F 2586 PHE cc_start: 0.9381 (t80) cc_final: 0.8889 (t80) outliers start: 394 outliers final: 160 residues processed: 1316 average time/residue: 1.0677 time to fit residues: 2500.5485 Evaluate side-chains 948 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 773 time to evaluate : 9.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 610 CYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1443 ILE Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 2183 TYR Chi-restraints excluded: chain A residue 2224 ASP Chi-restraints excluded: chain A residue 2231 LEU Chi-restraints excluded: chain A residue 2256 VAL Chi-restraints excluded: chain A residue 2409 LEU Chi-restraints excluded: chain A residue 2607 VAL Chi-restraints excluded: chain A residue 2666 LEU Chi-restraints excluded: chain A residue 2884 LYS Chi-restraints excluded: chain A residue 3021 ILE Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 954 TRP Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1331 MET Chi-restraints excluded: chain B residue 1403 HIS Chi-restraints excluded: chain B residue 1471 VAL Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1591 LEU Chi-restraints excluded: chain B residue 1695 VAL Chi-restraints excluded: chain B residue 1734 VAL Chi-restraints excluded: chain B residue 2183 TYR Chi-restraints excluded: chain B residue 2231 LEU Chi-restraints excluded: chain B residue 2513 ASP Chi-restraints excluded: chain B residue 2542 GLN Chi-restraints excluded: chain B residue 2607 VAL Chi-restraints excluded: chain B residue 2728 VAL Chi-restraints excluded: chain B residue 3012 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 954 TRP Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1243 ILE Chi-restraints excluded: chain C residue 1403 HIS Chi-restraints excluded: chain C residue 1526 ILE Chi-restraints excluded: chain C residue 1591 LEU Chi-restraints excluded: chain C residue 1679 LEU Chi-restraints excluded: chain C residue 1695 VAL Chi-restraints excluded: chain C residue 1734 VAL Chi-restraints excluded: chain C residue 2231 LEU Chi-restraints excluded: chain C residue 2254 MET Chi-restraints excluded: chain C residue 2268 LEU Chi-restraints excluded: chain C residue 2513 ASP Chi-restraints excluded: chain C residue 2607 VAL Chi-restraints excluded: chain C residue 2728 VAL Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 954 TRP Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1160 ASP Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1395 THR Chi-restraints excluded: chain D residue 1470 MET Chi-restraints excluded: chain D residue 1471 VAL Chi-restraints excluded: chain D residue 1640 LEU Chi-restraints excluded: chain D residue 1695 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2183 TYR Chi-restraints excluded: chain D residue 2231 LEU Chi-restraints excluded: chain D residue 2254 MET Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2409 LEU Chi-restraints excluded: chain D residue 2421 GLN Chi-restraints excluded: chain D residue 2513 ASP Chi-restraints excluded: chain D residue 2607 VAL Chi-restraints excluded: chain D residue 2728 VAL Chi-restraints excluded: chain D residue 3012 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain E residue 712 VAL Chi-restraints excluded: chain E residue 777 ASP Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 954 TRP Chi-restraints excluded: chain E residue 1047 VAL Chi-restraints excluded: chain E residue 1243 ILE Chi-restraints excluded: chain E residue 1252 LEU Chi-restraints excluded: chain E residue 1296 MET Chi-restraints excluded: chain E residue 1327 SER Chi-restraints excluded: chain E residue 1331 MET Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1403 HIS Chi-restraints excluded: chain E residue 1445 CYS Chi-restraints excluded: chain E residue 1449 VAL Chi-restraints excluded: chain E residue 1640 LEU Chi-restraints excluded: chain E residue 1695 VAL Chi-restraints excluded: chain E residue 2256 VAL Chi-restraints excluded: chain E residue 2258 LEU Chi-restraints excluded: chain E residue 2409 LEU Chi-restraints excluded: chain E residue 2421 GLN Chi-restraints excluded: chain E residue 2513 ASP Chi-restraints excluded: chain E residue 2607 VAL Chi-restraints excluded: chain E residue 2728 VAL Chi-restraints excluded: chain E residue 2884 LYS Chi-restraints excluded: chain E residue 3012 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 695 ILE Chi-restraints excluded: chain F residue 712 VAL Chi-restraints excluded: chain F residue 777 ASP Chi-restraints excluded: chain F residue 811 LEU Chi-restraints excluded: chain F residue 849 LEU Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 954 TRP Chi-restraints excluded: chain F residue 1047 VAL Chi-restraints excluded: chain F residue 1243 ILE Chi-restraints excluded: chain F residue 1331 MET Chi-restraints excluded: chain F residue 1403 HIS Chi-restraints excluded: chain F residue 1471 VAL Chi-restraints excluded: chain F residue 1497 ILE Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1695 VAL Chi-restraints excluded: chain F residue 2224 ASP Chi-restraints excluded: chain F residue 2421 GLN Chi-restraints excluded: chain F residue 2513 ASP Chi-restraints excluded: chain F residue 2552 ASP Chi-restraints excluded: chain F residue 2607 VAL Chi-restraints excluded: chain F residue 2728 VAL Chi-restraints excluded: chain F residue 3012 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1662 random chunks: chunk 838 optimal weight: 3.9990 chunk 468 optimal weight: 5.9990 chunk 1256 optimal weight: 5.9990 chunk 1027 optimal weight: 0.0020 chunk 416 optimal weight: 10.0000 chunk 1511 optimal weight: 7.9990 chunk 1633 optimal weight: 4.9990 chunk 1346 optimal weight: 7.9990 chunk 1499 optimal weight: 10.0000 chunk 515 optimal weight: 1.9990 chunk 1212 optimal weight: 8.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 585 HIS ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2537 HIS A2802 HIS A2821 GLN ** A3007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1403 HIS B2221 HIS ** B2421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2537 HIS ** B2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2821 GLN ** B3007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 ASN C 585 HIS C1625 GLN ** C1986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2821 GLN D1279 GLN D1388 HIS D1403 HIS D1625 GLN ** D1986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2221 HIS D2606 GLN D2821 GLN ** D3007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2221 HIS E2537 HIS E2821 GLN ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1403 HIS F2537 HIS ** F2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2821 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 127536 Z= 0.330 Angle : 0.691 10.543 173910 Z= 0.355 Chirality : 0.047 0.254 20016 Planarity : 0.005 0.070 22932 Dihedral : 5.734 56.088 18082 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.76 % Allowed : 9.27 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.13 % 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: -1.79 (0.06), residues: 16572 helix: 0.13 (0.06), residues: 7392 sheet: -1.83 (0.10), residues: 2052 loop : -2.44 (0.07), residues: 7128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B2605 HIS 0.025 0.002 HIS C1403 PHE 0.036 0.002 PHE C1983 TYR 0.025 0.002 TYR A2678 ARG 0.009 0.001 ARG B2584 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1279 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 482 poor density : 797 time to evaluate : 9.873 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: A 233 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7668 (mm) REVERT: A 475 MET cc_start: 0.9012 (mmm) cc_final: 0.8774 (mmm) REVERT: A 641 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8420 (p0) REVERT: A 684 MET cc_start: 0.8474 (mmm) cc_final: 0.7604 (mmm) REVERT: A 708 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9246 (tm) REVERT: A 710 ASP cc_start: 0.7658 (m-30) cc_final: 0.7225 (m-30) REVERT: A 811 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8084 (pp) REVERT: A 1184 GLU cc_start: 0.8314 (pm20) cc_final: 0.8045 (pm20) REVERT: A 1406 HIS cc_start: 0.8595 (t70) cc_final: 0.7599 (t70) REVERT: A 1470 MET cc_start: 0.8911 (ptm) cc_final: 0.8601 (ptm) REVERT: A 1498 ARG cc_start: 0.8790 (ttm170) cc_final: 0.8313 (ttp80) REVERT: A 1729 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8487 (mm-30) REVERT: A 2201 ASP cc_start: 0.7755 (m-30) cc_final: 0.7504 (m-30) REVERT: A 2251 GLU cc_start: 0.8869 (pp20) cc_final: 0.8254 (pm20) REVERT: A 2326 TRP cc_start: 0.7953 (t-100) cc_final: 0.7230 (t-100) REVERT: A 2411 MET cc_start: 0.5696 (ttp) cc_final: 0.5206 (mtt) REVERT: A 2490 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: A 2586 PHE cc_start: 0.9259 (t80) cc_final: 0.9054 (t80) REVERT: A 2650 ILE cc_start: 0.7413 (mp) cc_final: 0.7207 (tp) REVERT: A 2666 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8941 (mm) REVERT: B 317 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8326 (pp) REVERT: B 1140 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8343 (tm) REVERT: B 1626 GLU cc_start: 0.9197 (tt0) cc_final: 0.8961 (mt-10) REVERT: B 1654 MET cc_start: 0.9306 (ttp) cc_final: 0.8950 (ptm) REVERT: B 2367 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8325 (p) REVERT: B 2411 MET cc_start: 0.5658 (ttp) cc_final: 0.4921 (mtt) REVERT: B 2586 PHE cc_start: 0.9193 (t80) cc_final: 0.8978 (t80) REVERT: C 317 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.7922 (pp) REVERT: C 710 ASP cc_start: 0.7779 (m-30) cc_final: 0.7294 (m-30) REVERT: C 811 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7442 (pp) REVERT: C 1037 MET cc_start: 0.8892 (mmp) cc_final: 0.8508 (mmp) REVERT: C 1498 ARG cc_start: 0.8758 (ttm170) cc_final: 0.8314 (ttp80) REVERT: C 1591 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8641 (mt) REVERT: C 1629 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8512 (p0) REVERT: C 1654 MET cc_start: 0.9222 (ttp) cc_final: 0.8920 (ptm) REVERT: C 2375 MET cc_start: 0.9098 (tpp) cc_final: 0.8894 (tpp) REVERT: C 2411 MET cc_start: 0.6395 (ttp) cc_final: 0.5714 (mtt) REVERT: C 2586 PHE cc_start: 0.9330 (t80) cc_final: 0.9067 (t80) REVERT: C 2692 MET cc_start: 0.4967 (tmt) cc_final: 0.4080 (tmt) REVERT: D 317 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7622 (pp) REVERT: D 475 MET cc_start: 0.8949 (mmm) cc_final: 0.8741 (mmm) REVERT: D 811 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7943 (pp) REVERT: D 1037 MET cc_start: 0.8863 (mmp) cc_final: 0.8366 (mmp) REVERT: D 1646 TRP cc_start: 0.8969 (m-10) cc_final: 0.8492 (m-10) REVERT: D 1654 MET cc_start: 0.9416 (ttp) cc_final: 0.9075 (ptm) REVERT: D 2253 GLU cc_start: 0.8811 (pp20) cc_final: 0.8432 (pp20) REVERT: D 2254 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8880 (tmm) REVERT: D 2411 MET cc_start: 0.4674 (ttp) cc_final: 0.4163 (mtt) REVERT: D 2586 PHE cc_start: 0.9275 (t80) cc_final: 0.8842 (t80) REVERT: E 90 LEU cc_start: 0.8941 (tp) cc_final: 0.8723 (tt) REVERT: E 207 MET cc_start: 0.8709 (mtt) cc_final: 0.8414 (mtt) REVERT: E 305 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8655 (tp) REVERT: E 585 HIS cc_start: 0.7135 (t-170) cc_final: 0.6814 (t-170) REVERT: E 641 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8468 (p0) REVERT: E 710 ASP cc_start: 0.7607 (m-30) cc_final: 0.7243 (m-30) REVERT: E 1230 MET cc_start: 0.9287 (mmm) cc_final: 0.9085 (mmm) REVERT: E 1406 HIS cc_start: 0.7995 (t70) cc_final: 0.7390 (t70) REVERT: E 1535 GLN cc_start: 0.7906 (tp40) cc_final: 0.7397 (tp-100) REVERT: E 1646 TRP cc_start: 0.8992 (m-10) cc_final: 0.8532 (m-10) REVERT: E 1654 MET cc_start: 0.9419 (ttp) cc_final: 0.9086 (ptm) REVERT: E 1727 ASN cc_start: 0.8754 (t0) cc_final: 0.8473 (t0) REVERT: E 2036 ARG cc_start: 0.8487 (ptm-80) cc_final: 0.8234 (ppt170) REVERT: E 2411 MET cc_start: 0.5074 (ttp) cc_final: 0.4681 (mtt) REVERT: E 2490 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: E 2586 PHE cc_start: 0.9284 (t80) cc_final: 0.8975 (t80) REVERT: F 317 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8118 (pp) REVERT: F 1498 ARG cc_start: 0.8868 (ttm170) cc_final: 0.8296 (ttm-80) REVERT: F 1654 MET cc_start: 0.9352 (ttp) cc_final: 0.8958 (ptm) REVERT: F 2254 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8718 (tpp) REVERT: F 2411 MET cc_start: 0.5473 (ttp) cc_final: 0.4875 (mtt) REVERT: F 2586 PHE cc_start: 0.9377 (t80) cc_final: 0.8859 (t80) outliers start: 482 outliers final: 267 residues processed: 1207 average time/residue: 0.9675 time to fit residues: 2097.3630 Evaluate side-chains 1024 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 736 time to evaluate : 9.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 CYS Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1343 VAL Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2038 VAL Chi-restraints excluded: chain A residue 2101 SER Chi-restraints excluded: chain A residue 2183 TYR Chi-restraints excluded: chain A residue 2224 ASP Chi-restraints excluded: chain A residue 2231 LEU Chi-restraints excluded: chain A residue 2239 VAL Chi-restraints excluded: chain A residue 2256 VAL Chi-restraints excluded: chain A residue 2409 LEU Chi-restraints excluded: chain A residue 2421 GLN Chi-restraints excluded: chain A residue 2490 GLU Chi-restraints excluded: chain A residue 2607 VAL Chi-restraints excluded: chain A residue 2666 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2774 ASP Chi-restraints excluded: chain A residue 2884 LYS Chi-restraints excluded: chain A residue 2903 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1160 ASP Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1307 VAL Chi-restraints excluded: chain B residue 1327 SER Chi-restraints excluded: chain B residue 1395 THR Chi-restraints excluded: chain B residue 1432 MET Chi-restraints excluded: chain B residue 1471 VAL Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1591 LEU Chi-restraints excluded: chain B residue 1636 LEU Chi-restraints excluded: chain B residue 1699 VAL Chi-restraints excluded: chain B residue 1734 VAL Chi-restraints excluded: chain B residue 2183 TYR Chi-restraints excluded: chain B residue 2224 ASP Chi-restraints excluded: chain B residue 2275 ARG Chi-restraints excluded: chain B residue 2367 VAL Chi-restraints excluded: chain B residue 2513 ASP Chi-restraints excluded: chain B residue 2542 GLN Chi-restraints excluded: chain B residue 2607 VAL Chi-restraints excluded: chain B residue 2728 VAL Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2894 VAL Chi-restraints excluded: chain B residue 2946 VAL Chi-restraints excluded: chain B residue 3012 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1189 LEU Chi-restraints excluded: chain C residue 1243 ILE Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1265 LEU Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1327 SER Chi-restraints excluded: chain C residue 1331 MET Chi-restraints excluded: chain C residue 1526 ILE Chi-restraints excluded: chain C residue 1591 LEU Chi-restraints excluded: chain C residue 1629 ASP Chi-restraints excluded: chain C residue 1630 LEU Chi-restraints excluded: chain C residue 1640 LEU Chi-restraints excluded: chain C residue 1663 LEU Chi-restraints excluded: chain C residue 1699 VAL Chi-restraints excluded: chain C residue 1734 VAL Chi-restraints excluded: chain C residue 2194 MET Chi-restraints excluded: chain C residue 2224 ASP Chi-restraints excluded: chain C residue 2231 LEU Chi-restraints excluded: chain C residue 2409 LEU Chi-restraints excluded: chain C residue 2513 ASP Chi-restraints excluded: chain C residue 2607 VAL Chi-restraints excluded: chain C residue 2728 VAL Chi-restraints excluded: chain C residue 2894 VAL Chi-restraints excluded: chain C residue 2946 VAL Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1160 ASP Chi-restraints excluded: chain D residue 1189 LEU Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1252 LEU Chi-restraints excluded: chain D residue 1307 VAL Chi-restraints excluded: chain D residue 1331 MET Chi-restraints excluded: chain D residue 1395 THR Chi-restraints excluded: chain D residue 1449 VAL Chi-restraints excluded: chain D residue 1470 MET Chi-restraints excluded: chain D residue 1471 VAL Chi-restraints excluded: chain D residue 1526 ILE Chi-restraints excluded: chain D residue 1695 VAL Chi-restraints excluded: chain D residue 2183 TYR Chi-restraints excluded: chain D residue 2224 ASP Chi-restraints excluded: chain D residue 2254 MET Chi-restraints excluded: chain D residue 2256 VAL Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2409 LEU Chi-restraints excluded: chain D residue 2410 ASP Chi-restraints excluded: chain D residue 2421 GLN Chi-restraints excluded: chain D residue 2513 ASP Chi-restraints excluded: chain D residue 2607 VAL Chi-restraints excluded: chain D residue 2728 VAL Chi-restraints excluded: chain D residue 2762 LEU Chi-restraints excluded: chain D residue 2894 VAL Chi-restraints excluded: chain D residue 2946 VAL Chi-restraints excluded: chain D residue 3012 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain E residue 712 VAL Chi-restraints excluded: chain E residue 777 ASP Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 916 ILE Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 1047 VAL Chi-restraints excluded: chain E residue 1158 ASP Chi-restraints excluded: chain E residue 1160 ASP Chi-restraints excluded: chain E residue 1243 ILE Chi-restraints excluded: chain E residue 1252 LEU Chi-restraints excluded: chain E residue 1265 LEU Chi-restraints excluded: chain E residue 1296 MET Chi-restraints excluded: chain E residue 1307 VAL Chi-restraints excluded: chain E residue 1327 SER Chi-restraints excluded: chain E residue 1331 MET Chi-restraints excluded: chain E residue 1395 THR Chi-restraints excluded: chain E residue 1449 VAL Chi-restraints excluded: chain E residue 1464 LEU Chi-restraints excluded: chain E residue 1526 ILE Chi-restraints excluded: chain E residue 1567 LEU Chi-restraints excluded: chain E residue 1640 LEU Chi-restraints excluded: chain E residue 2038 VAL Chi-restraints excluded: chain E residue 2256 VAL Chi-restraints excluded: chain E residue 2258 LEU Chi-restraints excluded: chain E residue 2409 LEU Chi-restraints excluded: chain E residue 2410 ASP Chi-restraints excluded: chain E residue 2421 GLN Chi-restraints excluded: chain E residue 2438 ILE Chi-restraints excluded: chain E residue 2490 GLU Chi-restraints excluded: chain E residue 2513 ASP Chi-restraints excluded: chain E residue 2607 VAL Chi-restraints excluded: chain E residue 2728 VAL Chi-restraints excluded: chain E residue 2748 THR Chi-restraints excluded: chain E residue 2762 LEU Chi-restraints excluded: chain E residue 2884 LYS Chi-restraints excluded: chain E residue 2946 VAL Chi-restraints excluded: chain E residue 3012 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 695 ILE Chi-restraints excluded: chain F residue 712 VAL Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 777 ASP Chi-restraints excluded: chain F residue 849 LEU Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 1047 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1120 VAL Chi-restraints excluded: chain F residue 1158 ASP Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1181 THR Chi-restraints excluded: chain F residue 1243 ILE Chi-restraints excluded: chain F residue 1265 LEU Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1331 MET Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1432 MET Chi-restraints excluded: chain F residue 1471 VAL Chi-restraints excluded: chain F residue 1497 ILE Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1567 LEU Chi-restraints excluded: chain F residue 1591 LEU Chi-restraints excluded: chain F residue 1713 LEU Chi-restraints excluded: chain F residue 2183 TYR Chi-restraints excluded: chain F residue 2224 ASP Chi-restraints excluded: chain F residue 2239 VAL Chi-restraints excluded: chain F residue 2254 MET Chi-restraints excluded: chain F residue 2409 LEU Chi-restraints excluded: chain F residue 2421 GLN Chi-restraints excluded: chain F residue 2513 ASP Chi-restraints excluded: chain F residue 2542 GLN Chi-restraints excluded: chain F residue 2552 ASP Chi-restraints excluded: chain F residue 2607 VAL Chi-restraints excluded: chain F residue 2728 VAL Chi-restraints excluded: chain F residue 2762 LEU Chi-restraints excluded: chain F residue 2894 VAL Chi-restraints excluded: chain F residue 2946 VAL Chi-restraints excluded: chain F residue 3012 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1662 random chunks: chunk 1493 optimal weight: 0.2980 chunk 1136 optimal weight: 10.0000 chunk 784 optimal weight: 3.9990 chunk 167 optimal weight: 0.4980 chunk 721 optimal weight: 20.0000 chunk 1015 optimal weight: 8.9990 chunk 1517 optimal weight: 2.9990 chunk 1606 optimal weight: 0.6980 chunk 792 optimal weight: 3.9990 chunk 1438 optimal weight: 5.9990 chunk 432 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2821 GLN ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2821 GLN ** C1986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2537 HIS ** C2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2821 GLN D1279 GLN D1403 HIS ** D1986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2537 HIS D2821 GLN ** D3007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1279 GLN E1403 HIS E2821 GLN F 585 HIS ** F2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2821 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 127536 Z= 0.186 Angle : 0.621 11.559 173910 Z= 0.313 Chirality : 0.044 0.246 20016 Planarity : 0.005 0.069 22932 Dihedral : 5.376 50.812 18082 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.30 % Allowed : 10.80 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.06), residues: 16572 helix: 0.53 (0.06), residues: 7476 sheet: -1.73 (0.10), residues: 2178 loop : -2.24 (0.07), residues: 6918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 954 HIS 0.012 0.001 HIS D1403 PHE 0.026 0.001 PHE C1983 TYR 0.021 0.001 TYR A2678 ARG 0.008 0.000 ARG A2419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 423 poor density : 824 time to evaluate : 10.094 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: A 570 LYS cc_start: 0.8615 (mmmt) cc_final: 0.8376 (mmmt) REVERT: A 684 MET cc_start: 0.8457 (mmm) cc_final: 0.7677 (mmm) REVERT: A 811 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8010 (pt) REVERT: A 893 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7470 (p) REVERT: A 1147 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9069 (pp) REVERT: A 1470 MET cc_start: 0.9001 (ptm) cc_final: 0.8654 (ptm) REVERT: A 1498 ARG cc_start: 0.8798 (ttm170) cc_final: 0.8354 (ttp80) REVERT: A 1729 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8480 (mm-30) REVERT: A 2251 GLU cc_start: 0.8832 (pp20) cc_final: 0.8171 (pm20) REVERT: A 2252 MET cc_start: 0.9098 (tpt) cc_final: 0.8866 (tpt) REVERT: A 2411 MET cc_start: 0.5807 (ttp) cc_final: 0.5311 (mtt) REVERT: A 2586 PHE cc_start: 0.9321 (t80) cc_final: 0.8979 (t80) REVERT: A 2650 ILE cc_start: 0.7319 (mp) cc_final: 0.7100 (tp) REVERT: A 2666 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8891 (mm) REVERT: B 39 MET cc_start: 0.8941 (mmp) cc_final: 0.8717 (mmm) REVERT: B 317 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8267 (pp) REVERT: B 1478 MET cc_start: 0.8255 (ttm) cc_final: 0.7860 (ttp) REVERT: B 1626 GLU cc_start: 0.9197 (tt0) cc_final: 0.8967 (mt-10) REVERT: B 1654 MET cc_start: 0.9287 (ttp) cc_final: 0.8976 (ptm) REVERT: B 2336 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8409 (t) REVERT: B 2367 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8267 (p) REVERT: B 2411 MET cc_start: 0.5753 (ttp) cc_final: 0.5074 (mtt) REVERT: B 2692 MET cc_start: 0.4925 (tmt) cc_final: 0.4182 (tmm) REVERT: B 2774 ASP cc_start: 0.8277 (m-30) cc_final: 0.7749 (m-30) REVERT: C 317 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.7879 (pp) REVERT: C 811 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7391 (pt) REVERT: C 1037 MET cc_start: 0.8826 (mmp) cc_final: 0.8495 (mmp) REVERT: C 1140 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8314 (tp) REVERT: C 1498 ARG cc_start: 0.8758 (ttm170) cc_final: 0.8324 (ttp80) REVERT: C 1546 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8853 (pm20) REVERT: C 1629 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8509 (p0) REVERT: C 1654 MET cc_start: 0.9242 (ttp) cc_final: 0.8917 (ptm) REVERT: C 2411 MET cc_start: 0.6353 (ttp) cc_final: 0.5757 (mtt) REVERT: C 2586 PHE cc_start: 0.9314 (t80) cc_final: 0.8965 (t80) REVERT: C 2692 MET cc_start: 0.5005 (tmt) cc_final: 0.4157 (tmm) REVERT: C 2755 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7332 (mm-30) REVERT: D 35 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.9014 (p) REVERT: D 263 ARG cc_start: 0.8125 (tpp80) cc_final: 0.7674 (tpt-90) REVERT: D 475 MET cc_start: 0.8919 (mmm) cc_final: 0.8687 (mmm) REVERT: D 811 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7872 (pt) REVERT: D 1037 MET cc_start: 0.8782 (mmp) cc_final: 0.8435 (mmp) REVERT: D 1410 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8298 (t) REVERT: D 1498 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8293 (ttp80) REVERT: D 1646 TRP cc_start: 0.8980 (m-10) cc_final: 0.8480 (m-10) REVERT: D 1654 MET cc_start: 0.9394 (ttp) cc_final: 0.9054 (ptm) REVERT: D 2253 GLU cc_start: 0.8717 (pp20) cc_final: 0.8406 (pp20) REVERT: D 2254 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8824 (tmm) REVERT: D 2411 MET cc_start: 0.4578 (ttp) cc_final: 0.4048 (mtt) REVERT: D 2586 PHE cc_start: 0.9237 (t80) cc_final: 0.8813 (t80) REVERT: D 2671 SER cc_start: 0.7316 (t) cc_final: 0.6924 (m) REVERT: E 90 LEU cc_start: 0.8977 (tp) cc_final: 0.8723 (tt) REVERT: E 207 MET cc_start: 0.8578 (mtt) cc_final: 0.8282 (mtt) REVERT: E 305 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8594 (tp) REVERT: E 710 ASP cc_start: 0.7608 (m-30) cc_final: 0.7334 (m-30) REVERT: E 1140 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8369 (tm) REVERT: E 1230 MET cc_start: 0.9265 (mmm) cc_final: 0.9051 (mmm) REVERT: E 1252 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8845 (tp) REVERT: E 1406 HIS cc_start: 0.7982 (t70) cc_final: 0.7216 (t-170) REVERT: E 1535 GLN cc_start: 0.7919 (tp40) cc_final: 0.7384 (tp-100) REVERT: E 1646 TRP cc_start: 0.8887 (m-10) cc_final: 0.8475 (m-10) REVERT: E 1654 MET cc_start: 0.9406 (ttp) cc_final: 0.9104 (ptm) REVERT: E 1727 ASN cc_start: 0.8699 (t0) cc_final: 0.8442 (t0) REVERT: E 2254 MET cc_start: 0.9307 (tpp) cc_final: 0.9047 (tpp) REVERT: E 2411 MET cc_start: 0.5034 (ttp) cc_final: 0.4647 (mtt) REVERT: E 2586 PHE cc_start: 0.9283 (t80) cc_final: 0.8980 (t80) REVERT: E 2692 MET cc_start: 0.4689 (tmt) cc_final: 0.3816 (tmm) REVERT: F 317 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7991 (pp) REVERT: F 566 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8296 (tm-30) REVERT: F 1498 ARG cc_start: 0.8800 (ttm170) cc_final: 0.8261 (ttm-80) REVERT: F 1654 MET cc_start: 0.9339 (ttp) cc_final: 0.8936 (ptm) REVERT: F 2253 GLU cc_start: 0.8527 (pp20) cc_final: 0.8227 (pp20) REVERT: F 2254 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8536 (tpp) REVERT: F 2411 MET cc_start: 0.5363 (ttp) cc_final: 0.4772 (mtt) REVERT: F 2586 PHE cc_start: 0.9388 (t80) cc_final: 0.8871 (t80) REVERT: F 2692 MET cc_start: 0.5056 (tmt) cc_final: 0.4275 (tmm) outliers start: 423 outliers final: 225 residues processed: 1180 average time/residue: 0.9881 time to fit residues: 2085.3312 Evaluate side-chains 972 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 726 time to evaluate : 9.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 2038 VAL Chi-restraints excluded: chain A residue 2101 SER Chi-restraints excluded: chain A residue 2224 ASP Chi-restraints excluded: chain A residue 2231 LEU Chi-restraints excluded: chain A residue 2256 VAL Chi-restraints excluded: chain A residue 2409 LEU Chi-restraints excluded: chain A residue 2607 VAL Chi-restraints excluded: chain A residue 2666 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2884 LYS Chi-restraints excluded: chain A residue 2903 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1307 VAL Chi-restraints excluded: chain B residue 1331 MET Chi-restraints excluded: chain B residue 1432 MET Chi-restraints excluded: chain B residue 1471 VAL Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1591 LEU Chi-restraints excluded: chain B residue 1666 GLN Chi-restraints excluded: chain B residue 1699 VAL Chi-restraints excluded: chain B residue 1734 VAL Chi-restraints excluded: chain B residue 2183 TYR Chi-restraints excluded: chain B residue 2336 VAL Chi-restraints excluded: chain B residue 2367 VAL Chi-restraints excluded: chain B residue 2513 ASP Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2607 VAL Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2894 VAL Chi-restraints excluded: chain B residue 2946 VAL Chi-restraints excluded: chain B residue 3012 VAL Chi-restraints excluded: chain B residue 3051 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1140 LEU Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1189 LEU Chi-restraints excluded: chain C residue 1243 ILE Chi-restraints excluded: chain C residue 1265 LEU Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1331 MET Chi-restraints excluded: chain C residue 1471 VAL Chi-restraints excluded: chain C residue 1526 ILE Chi-restraints excluded: chain C residue 1546 GLU Chi-restraints excluded: chain C residue 1567 LEU Chi-restraints excluded: chain C residue 1591 LEU Chi-restraints excluded: chain C residue 1629 ASP Chi-restraints excluded: chain C residue 1630 LEU Chi-restraints excluded: chain C residue 1640 LEU Chi-restraints excluded: chain C residue 1666 GLN Chi-restraints excluded: chain C residue 1734 VAL Chi-restraints excluded: chain C residue 2194 MET Chi-restraints excluded: chain C residue 2513 ASP Chi-restraints excluded: chain C residue 2607 VAL Chi-restraints excluded: chain C residue 2894 VAL Chi-restraints excluded: chain C residue 2946 VAL Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3051 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 893 SER Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1160 ASP Chi-restraints excluded: chain D residue 1189 LEU Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1331 MET Chi-restraints excluded: chain D residue 1410 VAL Chi-restraints excluded: chain D residue 1470 MET Chi-restraints excluded: chain D residue 1526 ILE Chi-restraints excluded: chain D residue 1640 LEU Chi-restraints excluded: chain D residue 1695 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2183 TYR Chi-restraints excluded: chain D residue 2231 LEU Chi-restraints excluded: chain D residue 2254 MET Chi-restraints excluded: chain D residue 2256 VAL Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2268 LEU Chi-restraints excluded: chain D residue 2410 ASP Chi-restraints excluded: chain D residue 2513 ASP Chi-restraints excluded: chain D residue 2607 VAL Chi-restraints excluded: chain D residue 2894 VAL Chi-restraints excluded: chain D residue 2946 VAL Chi-restraints excluded: chain D residue 3012 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 712 VAL Chi-restraints excluded: chain E residue 745 THR Chi-restraints excluded: chain E residue 777 ASP Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 893 SER Chi-restraints excluded: chain E residue 916 ILE Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 1047 VAL Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1158 ASP Chi-restraints excluded: chain E residue 1160 ASP Chi-restraints excluded: chain E residue 1243 ILE Chi-restraints excluded: chain E residue 1252 LEU Chi-restraints excluded: chain E residue 1296 MET Chi-restraints excluded: chain E residue 1307 VAL Chi-restraints excluded: chain E residue 1319 VAL Chi-restraints excluded: chain E residue 1331 MET Chi-restraints excluded: chain E residue 1443 ILE Chi-restraints excluded: chain E residue 1445 CYS Chi-restraints excluded: chain E residue 1449 VAL Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1526 ILE Chi-restraints excluded: chain E residue 1545 LEU Chi-restraints excluded: chain E residue 1546 GLU Chi-restraints excluded: chain E residue 1567 LEU Chi-restraints excluded: chain E residue 1695 VAL Chi-restraints excluded: chain E residue 2224 ASP Chi-restraints excluded: chain E residue 2410 ASP Chi-restraints excluded: chain E residue 2421 GLN Chi-restraints excluded: chain E residue 2438 ILE Chi-restraints excluded: chain E residue 2513 ASP Chi-restraints excluded: chain E residue 2607 VAL Chi-restraints excluded: chain E residue 2762 LEU Chi-restraints excluded: chain E residue 2795 MET Chi-restraints excluded: chain E residue 2946 VAL Chi-restraints excluded: chain E residue 3012 VAL Chi-restraints excluded: chain E residue 3025 ASP Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 712 VAL Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 777 ASP Chi-restraints excluded: chain F residue 849 LEU Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 1047 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1158 ASP Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1189 LEU Chi-restraints excluded: chain F residue 1243 ILE Chi-restraints excluded: chain F residue 1265 LEU Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1331 MET Chi-restraints excluded: chain F residue 1432 MET Chi-restraints excluded: chain F residue 1471 VAL Chi-restraints excluded: chain F residue 1508 ASP Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1527 VAL Chi-restraints excluded: chain F residue 1567 LEU Chi-restraints excluded: chain F residue 1713 LEU Chi-restraints excluded: chain F residue 2183 TYR Chi-restraints excluded: chain F residue 2254 MET Chi-restraints excluded: chain F residue 2513 ASP Chi-restraints excluded: chain F residue 2542 GLN Chi-restraints excluded: chain F residue 2544 VAL Chi-restraints excluded: chain F residue 2607 VAL Chi-restraints excluded: chain F residue 2762 LEU Chi-restraints excluded: chain F residue 2894 VAL Chi-restraints excluded: chain F residue 2946 VAL Chi-restraints excluded: chain F residue 3012 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1662 random chunks: chunk 1337 optimal weight: 7.9990 chunk 911 optimal weight: 0.0980 chunk 23 optimal weight: 5.9990 chunk 1196 optimal weight: 0.7980 chunk 662 optimal weight: 0.0870 chunk 1370 optimal weight: 5.9990 chunk 1110 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 820 optimal weight: 5.9990 chunk 1441 optimal weight: 4.9990 chunk 405 optimal weight: 9.9990 overall best weight: 2.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1388 HIS ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2821 GLN ** C2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN D1403 HIS D2821 GLN ** E1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1403 HIS E2741 HIS E2821 GLN ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2221 HIS ** F2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2821 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 127536 Z= 0.250 Angle : 0.634 13.152 173910 Z= 0.319 Chirality : 0.045 0.256 20016 Planarity : 0.004 0.071 22932 Dihedral : 5.264 47.372 18081 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.37 % Allowed : 11.39 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.06), residues: 16572 helix: 0.74 (0.06), residues: 7446 sheet: -1.64 (0.10), residues: 2172 loop : -2.14 (0.07), residues: 6954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B2456 HIS 0.011 0.001 HIS D1403 PHE 0.022 0.001 PHE D1512 TYR 0.023 0.001 TYR A2678 ARG 0.012 0.000 ARG B1589 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 432 poor density : 760 time to evaluate : 10.112 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 684 MET cc_start: 0.8544 (mmm) cc_final: 0.7725 (mmm) REVERT: A 811 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7990 (pt) REVERT: A 1147 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9022 (pp) REVERT: A 1432 MET cc_start: 0.8933 (ttm) cc_final: 0.8714 (ttp) REVERT: A 1498 ARG cc_start: 0.8839 (ttm170) cc_final: 0.8411 (ttp80) REVERT: A 1729 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8513 (mm-30) REVERT: A 2251 GLU cc_start: 0.8869 (pp20) cc_final: 0.8147 (pm20) REVERT: A 2252 MET cc_start: 0.9144 (tpt) cc_final: 0.8922 (tpt) REVERT: A 2411 MET cc_start: 0.5658 (ttp) cc_final: 0.5142 (mtt) REVERT: A 2586 PHE cc_start: 0.9312 (t80) cc_final: 0.8943 (t80) REVERT: A 2650 ILE cc_start: 0.7428 (mp) cc_final: 0.7198 (tp) REVERT: A 2666 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8886 (mm) REVERT: A 2692 MET cc_start: 0.4394 (tmt) cc_final: 0.3302 (tmt) REVERT: B 39 MET cc_start: 0.8948 (mmp) cc_final: 0.8748 (mmm) REVERT: B 317 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8263 (pp) REVERT: B 1478 MET cc_start: 0.8499 (ttm) cc_final: 0.8147 (ttp) REVERT: B 1626 GLU cc_start: 0.9226 (tt0) cc_final: 0.9008 (mt-10) REVERT: B 1654 MET cc_start: 0.9267 (ttp) cc_final: 0.8984 (ptm) REVERT: B 2037 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8619 (mp) REVERT: B 2367 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8286 (p) REVERT: B 2375 MET cc_start: 0.8981 (tpp) cc_final: 0.8770 (tpt) REVERT: B 2411 MET cc_start: 0.5725 (ttp) cc_final: 0.5029 (mtt) REVERT: B 2692 MET cc_start: 0.4798 (tmt) cc_final: 0.3960 (tmm) REVERT: C 39 MET cc_start: 0.8997 (mmp) cc_final: 0.8602 (mmm) REVERT: C 317 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7888 (pp) REVERT: C 811 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7464 (pt) REVERT: C 1037 MET cc_start: 0.8874 (mmp) cc_final: 0.8466 (mmp) REVERT: C 1410 VAL cc_start: 0.9081 (p) cc_final: 0.8784 (t) REVERT: C 1498 ARG cc_start: 0.8812 (ttm170) cc_final: 0.8357 (ttp80) REVERT: C 1629 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8541 (p0) REVERT: C 1654 MET cc_start: 0.9280 (ttp) cc_final: 0.8948 (ptm) REVERT: C 2252 MET cc_start: 0.9116 (tpt) cc_final: 0.8835 (tpp) REVERT: C 2411 MET cc_start: 0.6324 (ttp) cc_final: 0.5694 (mtt) REVERT: C 2586 PHE cc_start: 0.9316 (t80) cc_final: 0.9044 (t80) REVERT: C 2692 MET cc_start: 0.4940 (tmt) cc_final: 0.3863 (tmt) REVERT: D 35 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.9025 (p) REVERT: D 263 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7791 (tpt-90) REVERT: D 305 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8508 (tp) REVERT: D 811 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7873 (pt) REVERT: D 1037 MET cc_start: 0.8847 (mmp) cc_final: 0.8474 (mmp) REVERT: D 1410 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8354 (t) REVERT: D 1498 ARG cc_start: 0.8720 (ttm170) cc_final: 0.8366 (ttp80) REVERT: D 1646 TRP cc_start: 0.8992 (m-10) cc_final: 0.8661 (m-10) REVERT: D 1654 MET cc_start: 0.9401 (ttp) cc_final: 0.9074 (ptm) REVERT: D 2253 GLU cc_start: 0.8694 (pp20) cc_final: 0.8386 (pp20) REVERT: D 2254 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8778 (tmm) REVERT: D 2411 MET cc_start: 0.4584 (ttp) cc_final: 0.4006 (mtt) REVERT: D 2586 PHE cc_start: 0.9259 (t80) cc_final: 0.8818 (t80) REVERT: E 90 LEU cc_start: 0.8900 (tp) cc_final: 0.8584 (tt) REVERT: E 207 MET cc_start: 0.8570 (mtt) cc_final: 0.8216 (mtt) REVERT: E 305 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8590 (tp) REVERT: E 710 ASP cc_start: 0.7669 (m-30) cc_final: 0.7356 (m-30) REVERT: E 1147 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8897 (pp) REVERT: E 1230 MET cc_start: 0.9237 (mmm) cc_final: 0.9011 (mmm) REVERT: E 1252 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8882 (tp) REVERT: E 1406 HIS cc_start: 0.7999 (t70) cc_final: 0.7229 (t-90) REVERT: E 1535 GLN cc_start: 0.7955 (tp40) cc_final: 0.7394 (tp-100) REVERT: E 1654 MET cc_start: 0.9402 (ttp) cc_final: 0.9169 (ptm) REVERT: E 2253 GLU cc_start: 0.8563 (pp20) cc_final: 0.8307 (pp20) REVERT: E 2254 MET cc_start: 0.9278 (tpp) cc_final: 0.8878 (tpp) REVERT: E 2411 MET cc_start: 0.5025 (ttp) cc_final: 0.4613 (mtt) REVERT: E 2586 PHE cc_start: 0.9329 (t80) cc_final: 0.9010 (t80) REVERT: F 317 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7990 (pp) REVERT: F 566 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8253 (tm-30) REVERT: F 710 ASP cc_start: 0.7918 (m-30) cc_final: 0.7630 (m-30) REVERT: F 1410 VAL cc_start: 0.9102 (p) cc_final: 0.8839 (t) REVERT: F 1498 ARG cc_start: 0.8854 (ttm170) cc_final: 0.8350 (ttp80) REVERT: F 1654 MET cc_start: 0.9326 (ttp) cc_final: 0.8965 (ptm) REVERT: F 2037 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8718 (mp) REVERT: F 2253 GLU cc_start: 0.8498 (pp20) cc_final: 0.8242 (pp20) REVERT: F 2254 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8468 (tpp) REVERT: F 2411 MET cc_start: 0.5380 (ttp) cc_final: 0.4768 (mtt) REVERT: F 2586 PHE cc_start: 0.9387 (t80) cc_final: 0.8865 (t80) REVERT: F 2666 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8763 (mm) REVERT: F 2692 MET cc_start: 0.4871 (tmt) cc_final: 0.3924 (tmm) outliers start: 432 outliers final: 301 residues processed: 1124 average time/residue: 0.9554 time to fit residues: 1929.0942 Evaluate side-chains 1038 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 716 time to evaluate : 9.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 CYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1403 HIS Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2038 VAL Chi-restraints excluded: chain A residue 2101 SER Chi-restraints excluded: chain A residue 2224 ASP Chi-restraints excluded: chain A residue 2231 LEU Chi-restraints excluded: chain A residue 2410 ASP Chi-restraints excluded: chain A residue 2421 GLN Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2593 HIS Chi-restraints excluded: chain A residue 2607 VAL Chi-restraints excluded: chain A residue 2646 MET Chi-restraints excluded: chain A residue 2666 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2833 LEU Chi-restraints excluded: chain A residue 2884 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 893 SER Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1160 ASP Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1307 VAL Chi-restraints excluded: chain B residue 1327 SER Chi-restraints excluded: chain B residue 1331 MET Chi-restraints excluded: chain B residue 1432 MET Chi-restraints excluded: chain B residue 1471 VAL Chi-restraints excluded: chain B residue 1508 ASP Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1591 LEU Chi-restraints excluded: chain B residue 1666 GLN Chi-restraints excluded: chain B residue 1695 VAL Chi-restraints excluded: chain B residue 1699 VAL Chi-restraints excluded: chain B residue 1734 VAL Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2183 TYR Chi-restraints excluded: chain B residue 2224 ASP Chi-restraints excluded: chain B residue 2367 VAL Chi-restraints excluded: chain B residue 2513 ASP Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2607 VAL Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2894 VAL Chi-restraints excluded: chain B residue 2946 VAL Chi-restraints excluded: chain B residue 3012 VAL Chi-restraints excluded: chain B residue 3051 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 893 SER Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1189 LEU Chi-restraints excluded: chain C residue 1243 ILE Chi-restraints excluded: chain C residue 1265 LEU Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1319 VAL Chi-restraints excluded: chain C residue 1331 MET Chi-restraints excluded: chain C residue 1526 ILE Chi-restraints excluded: chain C residue 1567 LEU Chi-restraints excluded: chain C residue 1591 LEU Chi-restraints excluded: chain C residue 1629 ASP Chi-restraints excluded: chain C residue 1630 LEU Chi-restraints excluded: chain C residue 1640 LEU Chi-restraints excluded: chain C residue 1666 GLN Chi-restraints excluded: chain C residue 1699 VAL Chi-restraints excluded: chain C residue 1734 VAL Chi-restraints excluded: chain C residue 2194 MET Chi-restraints excluded: chain C residue 2224 ASP Chi-restraints excluded: chain C residue 2513 ASP Chi-restraints excluded: chain C residue 2607 VAL Chi-restraints excluded: chain C residue 2833 LEU Chi-restraints excluded: chain C residue 2894 VAL Chi-restraints excluded: chain C residue 2946 VAL Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 893 SER Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1160 ASP Chi-restraints excluded: chain D residue 1189 LEU Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1403 HIS Chi-restraints excluded: chain D residue 1410 VAL Chi-restraints excluded: chain D residue 1449 VAL Chi-restraints excluded: chain D residue 1471 VAL Chi-restraints excluded: chain D residue 1503 ASP Chi-restraints excluded: chain D residue 1508 ASP Chi-restraints excluded: chain D residue 1526 ILE Chi-restraints excluded: chain D residue 1545 LEU Chi-restraints excluded: chain D residue 1640 LEU Chi-restraints excluded: chain D residue 1734 VAL Chi-restraints excluded: chain D residue 2183 TYR Chi-restraints excluded: chain D residue 2224 ASP Chi-restraints excluded: chain D residue 2231 LEU Chi-restraints excluded: chain D residue 2254 MET Chi-restraints excluded: chain D residue 2256 VAL Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2268 LEU Chi-restraints excluded: chain D residue 2410 ASP Chi-restraints excluded: chain D residue 2513 ASP Chi-restraints excluded: chain D residue 2607 VAL Chi-restraints excluded: chain D residue 2762 LEU Chi-restraints excluded: chain D residue 2833 LEU Chi-restraints excluded: chain D residue 2894 VAL Chi-restraints excluded: chain D residue 2946 VAL Chi-restraints excluded: chain D residue 3012 VAL Chi-restraints excluded: chain D residue 3051 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 712 VAL Chi-restraints excluded: chain E residue 777 ASP Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 893 SER Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 916 ILE Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 1047 VAL Chi-restraints excluded: chain E residue 1147 LEU Chi-restraints excluded: chain E residue 1158 ASP Chi-restraints excluded: chain E residue 1243 ILE Chi-restraints excluded: chain E residue 1252 LEU Chi-restraints excluded: chain E residue 1265 LEU Chi-restraints excluded: chain E residue 1296 MET Chi-restraints excluded: chain E residue 1307 VAL Chi-restraints excluded: chain E residue 1319 VAL Chi-restraints excluded: chain E residue 1327 SER Chi-restraints excluded: chain E residue 1331 MET Chi-restraints excluded: chain E residue 1403 HIS Chi-restraints excluded: chain E residue 1443 ILE Chi-restraints excluded: chain E residue 1445 CYS Chi-restraints excluded: chain E residue 1449 VAL Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1508 ASP Chi-restraints excluded: chain E residue 1526 ILE Chi-restraints excluded: chain E residue 1567 LEU Chi-restraints excluded: chain E residue 1591 LEU Chi-restraints excluded: chain E residue 1640 LEU Chi-restraints excluded: chain E residue 2224 ASP Chi-restraints excluded: chain E residue 2231 LEU Chi-restraints excluded: chain E residue 2256 VAL Chi-restraints excluded: chain E residue 2258 LEU Chi-restraints excluded: chain E residue 2410 ASP Chi-restraints excluded: chain E residue 2438 ILE Chi-restraints excluded: chain E residue 2513 ASP Chi-restraints excluded: chain E residue 2542 GLN Chi-restraints excluded: chain E residue 2607 VAL Chi-restraints excluded: chain E residue 2748 THR Chi-restraints excluded: chain E residue 2762 LEU Chi-restraints excluded: chain E residue 2795 MET Chi-restraints excluded: chain E residue 2833 LEU Chi-restraints excluded: chain E residue 2884 LYS Chi-restraints excluded: chain E residue 2946 VAL Chi-restraints excluded: chain E residue 3012 VAL Chi-restraints excluded: chain E residue 3025 ASP Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 712 VAL Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 777 ASP Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 849 LEU Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 893 SER Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 1047 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1120 VAL Chi-restraints excluded: chain F residue 1158 ASP Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1189 LEU Chi-restraints excluded: chain F residue 1243 ILE Chi-restraints excluded: chain F residue 1265 LEU Chi-restraints excluded: chain F residue 1266 SER Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1327 SER Chi-restraints excluded: chain F residue 1331 MET Chi-restraints excluded: chain F residue 1432 MET Chi-restraints excluded: chain F residue 1471 VAL Chi-restraints excluded: chain F residue 1508 ASP Chi-restraints excluded: chain F residue 1567 LEU Chi-restraints excluded: chain F residue 1695 VAL Chi-restraints excluded: chain F residue 1699 VAL Chi-restraints excluded: chain F residue 1713 LEU Chi-restraints excluded: chain F residue 2037 LEU Chi-restraints excluded: chain F residue 2038 VAL Chi-restraints excluded: chain F residue 2066 LEU Chi-restraints excluded: chain F residue 2183 TYR Chi-restraints excluded: chain F residue 2224 ASP Chi-restraints excluded: chain F residue 2254 MET Chi-restraints excluded: chain F residue 2256 VAL Chi-restraints excluded: chain F residue 2513 ASP Chi-restraints excluded: chain F residue 2542 GLN Chi-restraints excluded: chain F residue 2544 VAL Chi-restraints excluded: chain F residue 2607 VAL Chi-restraints excluded: chain F residue 2666 LEU Chi-restraints excluded: chain F residue 2762 LEU Chi-restraints excluded: chain F residue 2894 VAL Chi-restraints excluded: chain F residue 2946 VAL Chi-restraints excluded: chain F residue 3012 VAL Chi-restraints excluded: chain F residue 3051 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1662 random chunks: chunk 540 optimal weight: 0.0770 chunk 1446 optimal weight: 4.9990 chunk 317 optimal weight: 0.8980 chunk 943 optimal weight: 9.9990 chunk 396 optimal weight: 2.9990 chunk 1608 optimal weight: 1.9990 chunk 1334 optimal weight: 0.0970 chunk 744 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 531 optimal weight: 0.9980 chunk 844 optimal weight: 10.0000 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 GLN ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2221 HIS A2327 HIS ** A2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 GLN B1625 GLN ** B2421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2821 GLN C 803 GLN ** C2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 803 GLN D2821 GLN E 803 GLN ** E1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1403 HIS E2821 GLN F 803 GLN F1625 GLN F2593 HIS F2821 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 127536 Z= 0.159 Angle : 0.600 13.833 173910 Z= 0.298 Chirality : 0.043 0.246 20016 Planarity : 0.004 0.071 22932 Dihedral : 5.026 43.655 18081 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.94 % Allowed : 12.39 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.05 % 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: -0.90 (0.07), residues: 16572 helix: 0.96 (0.06), residues: 7428 sheet: -1.54 (0.11), residues: 2190 loop : -2.03 (0.07), residues: 6954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 954 HIS 0.034 0.001 HIS E1403 PHE 0.019 0.001 PHE C3005 TYR 0.018 0.001 TYR A2183 ARG 0.006 0.000 ARG C2275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 377 poor density : 810 time to evaluate : 10.019 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 35 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8940 (p) REVERT: A 570 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8284 (mmmt) REVERT: A 738 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: A 811 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7933 (pt) REVERT: A 1147 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8978 (pp) REVERT: A 1498 ARG cc_start: 0.8832 (ttm170) cc_final: 0.8428 (ttp80) REVERT: A 1729 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8470 (mm-30) REVERT: A 2251 GLU cc_start: 0.8837 (pp20) cc_final: 0.8181 (pm20) REVERT: A 2253 GLU cc_start: 0.8280 (pp20) cc_final: 0.8029 (pp20) REVERT: A 2410 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8039 (t70) REVERT: A 2411 MET cc_start: 0.5727 (ttp) cc_final: 0.5222 (mtt) REVERT: A 2586 PHE cc_start: 0.9291 (t80) cc_final: 0.8919 (t80) REVERT: A 2666 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8835 (mm) REVERT: A 2692 MET cc_start: 0.4557 (tmt) cc_final: 0.3442 (tmt) REVERT: B 39 MET cc_start: 0.9019 (mmp) cc_final: 0.8779 (mmm) REVERT: B 317 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8264 (pp) REVERT: B 566 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8262 (tm-30) REVERT: B 595 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8624 (mp) REVERT: B 1410 VAL cc_start: 0.9008 (p) cc_final: 0.8642 (m) REVERT: B 1478 MET cc_start: 0.8455 (ttm) cc_final: 0.8124 (ttp) REVERT: B 1626 GLU cc_start: 0.9216 (tt0) cc_final: 0.8980 (mt-10) REVERT: B 1654 MET cc_start: 0.9241 (ttp) cc_final: 0.8992 (ptm) REVERT: B 2037 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8434 (mp) REVERT: B 2253 GLU cc_start: 0.8347 (pp20) cc_final: 0.7915 (pt0) REVERT: B 2367 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8244 (p) REVERT: B 2411 MET cc_start: 0.5627 (ttp) cc_final: 0.4931 (mtt) REVERT: B 2692 MET cc_start: 0.4896 (tmt) cc_final: 0.3983 (tmm) REVERT: C 39 MET cc_start: 0.8968 (mmp) cc_final: 0.8693 (mmm) REVERT: C 273 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8217 (tpp80) REVERT: C 317 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.7925 (pp) REVERT: C 738 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7061 (m-80) REVERT: C 811 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7434 (pt) REVERT: C 1037 MET cc_start: 0.8782 (mmp) cc_final: 0.8417 (mmp) REVERT: C 1410 VAL cc_start: 0.9037 (p) cc_final: 0.8688 (m) REVERT: C 1498 ARG cc_start: 0.8810 (ttm170) cc_final: 0.8354 (ttp80) REVERT: C 1591 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8672 (mp) REVERT: C 1629 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8518 (p0) REVERT: C 1654 MET cc_start: 0.9233 (ttp) cc_final: 0.8984 (ptm) REVERT: C 2252 MET cc_start: 0.9104 (tpt) cc_final: 0.8875 (tpp) REVERT: C 2253 GLU cc_start: 0.8324 (pp20) cc_final: 0.8069 (pp20) REVERT: C 2411 MET cc_start: 0.6281 (ttp) cc_final: 0.5685 (mtt) REVERT: C 2422 MET cc_start: 0.8320 (ttp) cc_final: 0.7913 (ptp) REVERT: C 2586 PHE cc_start: 0.9292 (t80) cc_final: 0.8930 (t80) REVERT: C 2692 MET cc_start: 0.4792 (tmt) cc_final: 0.3853 (tmm) REVERT: D 35 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8909 (p) REVERT: D 263 ARG cc_start: 0.8258 (tpp80) cc_final: 0.7851 (tpt-90) REVERT: D 305 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8475 (tp) REVERT: D 566 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8141 (tm-30) REVERT: D 738 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: D 811 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7863 (pt) REVERT: D 1037 MET cc_start: 0.8708 (mmp) cc_final: 0.8436 (mmp) REVERT: D 1410 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8246 (t) REVERT: D 1498 ARG cc_start: 0.8753 (ttm170) cc_final: 0.8401 (ttp80) REVERT: D 1546 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.9007 (pm20) REVERT: D 1587 PHE cc_start: 0.7923 (t80) cc_final: 0.7722 (t80) REVERT: D 1646 TRP cc_start: 0.8953 (m-10) cc_final: 0.8609 (m-10) REVERT: D 1654 MET cc_start: 0.9388 (ttp) cc_final: 0.9064 (ptm) REVERT: D 2253 GLU cc_start: 0.8612 (pp20) cc_final: 0.8164 (pp20) REVERT: D 2254 MET cc_start: 0.9059 (tmt) cc_final: 0.8698 (tmm) REVERT: D 2410 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7253 (t0) REVERT: D 2411 MET cc_start: 0.4367 (ttp) cc_final: 0.3901 (mtt) REVERT: D 2586 PHE cc_start: 0.9234 (t80) cc_final: 0.8800 (t80) REVERT: D 2692 MET cc_start: 0.5251 (tmt) cc_final: 0.4186 (tmm) REVERT: E 90 LEU cc_start: 0.8798 (tp) cc_final: 0.8468 (tt) REVERT: E 207 MET cc_start: 0.8473 (mtt) cc_final: 0.8165 (mtt) REVERT: E 305 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8573 (tp) REVERT: E 710 ASP cc_start: 0.7600 (m-30) cc_final: 0.7292 (m-30) REVERT: E 738 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: E 1147 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8893 (pp) REVERT: E 1406 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.7218 (t-90) REVERT: E 1535 GLN cc_start: 0.7933 (tp40) cc_final: 0.7354 (tp-100) REVERT: E 1654 MET cc_start: 0.9405 (ttp) cc_final: 0.9129 (ptm) REVERT: E 2254 MET cc_start: 0.9258 (tpp) cc_final: 0.8667 (tpp) REVERT: E 2411 MET cc_start: 0.5048 (ttp) cc_final: 0.4606 (mtt) REVERT: E 2586 PHE cc_start: 0.9316 (t80) cc_final: 0.9014 (t80) REVERT: E 2671 SER cc_start: 0.7232 (t) cc_final: 0.6995 (p) REVERT: F 317 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7987 (pp) REVERT: F 566 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8270 (tm-30) REVERT: F 1410 VAL cc_start: 0.9056 (p) cc_final: 0.8786 (t) REVERT: F 1498 ARG cc_start: 0.8853 (ttm170) cc_final: 0.8361 (ttp80) REVERT: F 1654 MET cc_start: 0.9276 (ttp) cc_final: 0.8983 (ptm) REVERT: F 2037 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8638 (mp) REVERT: F 2253 GLU cc_start: 0.8200 (pp20) cc_final: 0.7969 (pp20) REVERT: F 2254 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8226 (tpp) REVERT: F 2411 MET cc_start: 0.5255 (ttp) cc_final: 0.4760 (mtt) REVERT: F 2586 PHE cc_start: 0.9373 (t80) cc_final: 0.8859 (t80) REVERT: F 2666 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8735 (mm) REVERT: F 2692 MET cc_start: 0.4837 (tmt) cc_final: 0.3800 (tmm) outliers start: 377 outliers final: 238 residues processed: 1132 average time/residue: 1.0180 time to fit residues: 2072.7507 Evaluate side-chains 1005 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 736 time to evaluate : 9.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 610 CYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1403 HIS Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2038 VAL Chi-restraints excluded: chain A residue 2410 ASP Chi-restraints excluded: chain A residue 2421 GLN Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2593 HIS Chi-restraints excluded: chain A residue 2607 VAL Chi-restraints excluded: chain A residue 2646 MET Chi-restraints excluded: chain A residue 2666 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1160 ASP Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1307 VAL Chi-restraints excluded: chain B residue 1331 MET Chi-restraints excluded: chain B residue 1471 VAL Chi-restraints excluded: chain B residue 1508 ASP Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1666 GLN Chi-restraints excluded: chain B residue 1695 VAL Chi-restraints excluded: chain B residue 1699 VAL Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2183 TYR Chi-restraints excluded: chain B residue 2367 VAL Chi-restraints excluded: chain B residue 2513 ASP Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2607 VAL Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2894 VAL Chi-restraints excluded: chain B residue 2946 VAL Chi-restraints excluded: chain B residue 3012 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 738 PHE Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 893 SER Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1243 ILE Chi-restraints excluded: chain C residue 1265 LEU Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1319 VAL Chi-restraints excluded: chain C residue 1331 MET Chi-restraints excluded: chain C residue 1526 ILE Chi-restraints excluded: chain C residue 1567 LEU Chi-restraints excluded: chain C residue 1591 LEU Chi-restraints excluded: chain C residue 1629 ASP Chi-restraints excluded: chain C residue 1630 LEU Chi-restraints excluded: chain C residue 1666 GLN Chi-restraints excluded: chain C residue 1699 VAL Chi-restraints excluded: chain C residue 2194 MET Chi-restraints excluded: chain C residue 2513 ASP Chi-restraints excluded: chain C residue 2607 VAL Chi-restraints excluded: chain C residue 2894 VAL Chi-restraints excluded: chain C residue 2946 VAL Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3051 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 738 PHE Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1160 ASP Chi-restraints excluded: chain D residue 1189 LEU Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1410 VAL Chi-restraints excluded: chain D residue 1449 VAL Chi-restraints excluded: chain D residue 1526 ILE Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1640 LEU Chi-restraints excluded: chain D residue 1695 VAL Chi-restraints excluded: chain D residue 1734 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2183 TYR Chi-restraints excluded: chain D residue 2231 LEU Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2410 ASP Chi-restraints excluded: chain D residue 2513 ASP Chi-restraints excluded: chain D residue 2607 VAL Chi-restraints excluded: chain D residue 2748 THR Chi-restraints excluded: chain D residue 2894 VAL Chi-restraints excluded: chain D residue 2946 VAL Chi-restraints excluded: chain D residue 3012 VAL Chi-restraints excluded: chain D residue 3051 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 738 PHE Chi-restraints excluded: chain E residue 777 ASP Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 916 ILE Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 1047 VAL Chi-restraints excluded: chain E residue 1147 LEU Chi-restraints excluded: chain E residue 1243 ILE Chi-restraints excluded: chain E residue 1265 LEU Chi-restraints excluded: chain E residue 1307 VAL Chi-restraints excluded: chain E residue 1319 VAL Chi-restraints excluded: chain E residue 1331 MET Chi-restraints excluded: chain E residue 1406 HIS Chi-restraints excluded: chain E residue 1443 ILE Chi-restraints excluded: chain E residue 1445 CYS Chi-restraints excluded: chain E residue 1449 VAL Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1526 ILE Chi-restraints excluded: chain E residue 1545 LEU Chi-restraints excluded: chain E residue 1567 LEU Chi-restraints excluded: chain E residue 1640 LEU Chi-restraints excluded: chain E residue 1695 VAL Chi-restraints excluded: chain E residue 2258 LEU Chi-restraints excluded: chain E residue 2409 LEU Chi-restraints excluded: chain E residue 2410 ASP Chi-restraints excluded: chain E residue 2438 ILE Chi-restraints excluded: chain E residue 2513 ASP Chi-restraints excluded: chain E residue 2544 VAL Chi-restraints excluded: chain E residue 2607 VAL Chi-restraints excluded: chain E residue 2762 LEU Chi-restraints excluded: chain E residue 2795 MET Chi-restraints excluded: chain E residue 2946 VAL Chi-restraints excluded: chain E residue 3012 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 777 ASP Chi-restraints excluded: chain F residue 849 LEU Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 893 SER Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 1047 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1189 LEU Chi-restraints excluded: chain F residue 1243 ILE Chi-restraints excluded: chain F residue 1265 LEU Chi-restraints excluded: chain F residue 1266 SER Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1319 VAL Chi-restraints excluded: chain F residue 1331 MET Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1471 VAL Chi-restraints excluded: chain F residue 1508 ASP Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1567 LEU Chi-restraints excluded: chain F residue 1666 GLN Chi-restraints excluded: chain F residue 1695 VAL Chi-restraints excluded: chain F residue 1699 VAL Chi-restraints excluded: chain F residue 1713 LEU Chi-restraints excluded: chain F residue 2037 LEU Chi-restraints excluded: chain F residue 2183 TYR Chi-restraints excluded: chain F residue 2254 MET Chi-restraints excluded: chain F residue 2275 ARG Chi-restraints excluded: chain F residue 2513 ASP Chi-restraints excluded: chain F residue 2544 VAL Chi-restraints excluded: chain F residue 2593 HIS Chi-restraints excluded: chain F residue 2607 VAL Chi-restraints excluded: chain F residue 2666 LEU Chi-restraints excluded: chain F residue 2762 LEU Chi-restraints excluded: chain F residue 2894 VAL Chi-restraints excluded: chain F residue 2946 VAL Chi-restraints excluded: chain F residue 3012 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1662 random chunks: chunk 1550 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 916 optimal weight: 0.8980 chunk 1174 optimal weight: 9.9990 chunk 909 optimal weight: 0.7980 chunk 1353 optimal weight: 9.9990 chunk 897 optimal weight: 0.7980 chunk 1601 optimal weight: 0.0000 chunk 1002 optimal weight: 5.9990 chunk 976 optimal weight: 40.0000 chunk 739 optimal weight: 0.0770 overall best weight: 0.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS A1405 HIS A1418 GLN A2211 GLN A2741 HIS ** A2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2211 GLN B2741 HIS ** B2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS C2327 HIS ** C2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1403 HIS D2327 HIS ** D2421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1403 HIS E2327 HIS F2741 HIS F2821 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 127536 Z= 0.150 Angle : 0.591 13.756 173910 Z= 0.291 Chirality : 0.043 0.244 20016 Planarity : 0.004 0.071 22932 Dihedral : 4.825 39.381 18081 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.94 % Allowed : 12.61 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.04 % 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: -0.72 (0.07), residues: 16572 helix: 1.10 (0.06), residues: 7446 sheet: -1.43 (0.11), residues: 2130 loop : -1.95 (0.07), residues: 6996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A2326 HIS 0.021 0.001 HIS F2593 PHE 0.034 0.001 PHE B1512 TYR 0.018 0.001 TYR A2183 ARG 0.015 0.000 ARG F2280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 824 time to evaluate : 9.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8917 (p) REVERT: A 570 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8303 (mmmt) REVERT: A 738 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: A 811 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7884 (pt) REVERT: A 1147 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8950 (pp) REVERT: A 1191 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8081 (pmm150) REVERT: A 1406 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.7669 (t-90) REVERT: A 1498 ARG cc_start: 0.8896 (ttm170) cc_final: 0.8433 (ttp80) REVERT: A 1729 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8510 (mm-30) REVERT: A 2251 GLU cc_start: 0.8829 (pp20) cc_final: 0.8191 (pm20) REVERT: A 2410 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8157 (t70) REVERT: A 2411 MET cc_start: 0.5557 (ttp) cc_final: 0.5208 (mtt) REVERT: A 2586 PHE cc_start: 0.9263 (t80) cc_final: 0.8859 (t80) REVERT: A 2666 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8834 (mm) REVERT: A 2692 MET cc_start: 0.4426 (tmt) cc_final: 0.3231 (tmm) REVERT: B 317 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8261 (pp) REVERT: B 738 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6081 (m-80) REVERT: B 1410 VAL cc_start: 0.8963 (p) cc_final: 0.8601 (m) REVERT: B 1591 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8591 (mp) REVERT: B 1626 GLU cc_start: 0.9156 (tt0) cc_final: 0.8884 (mt-10) REVERT: B 1654 MET cc_start: 0.9235 (ttp) cc_final: 0.8999 (ptm) REVERT: B 2037 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8487 (mp) REVERT: B 2249 ARG cc_start: 0.8706 (ttp-170) cc_final: 0.8277 (ptm160) REVERT: B 2253 GLU cc_start: 0.8225 (pp20) cc_final: 0.7999 (pt0) REVERT: B 2254 MET cc_start: 0.8584 (tmm) cc_final: 0.8186 (tmm) REVERT: B 2367 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8237 (p) REVERT: B 2411 MET cc_start: 0.5412 (ttp) cc_final: 0.4879 (mtt) REVERT: B 2692 MET cc_start: 0.4953 (tmt) cc_final: 0.4025 (tmm) REVERT: C 39 MET cc_start: 0.9027 (mmp) cc_final: 0.8700 (mmm) REVERT: C 273 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8193 (tpp80) REVERT: C 317 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7935 (pp) REVERT: C 738 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.6985 (m-80) REVERT: C 811 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7472 (pt) REVERT: C 1037 MET cc_start: 0.8790 (mmp) cc_final: 0.8406 (mmp) REVERT: C 1410 VAL cc_start: 0.9032 (p) cc_final: 0.8669 (m) REVERT: C 1498 ARG cc_start: 0.8825 (ttm170) cc_final: 0.8373 (ttp80) REVERT: C 1591 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8632 (mp) REVERT: C 1629 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8588 (p0) REVERT: C 2252 MET cc_start: 0.9089 (tpt) cc_final: 0.8852 (tpp) REVERT: C 2410 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.7804 (t0) REVERT: C 2411 MET cc_start: 0.6173 (ttp) cc_final: 0.5530 (mtt) REVERT: C 2422 MET cc_start: 0.8318 (ttp) cc_final: 0.7943 (ptp) REVERT: C 2526 MET cc_start: 0.8539 (mmm) cc_final: 0.8329 (tpp) REVERT: C 2586 PHE cc_start: 0.9274 (t80) cc_final: 0.8910 (t80) REVERT: C 2692 MET cc_start: 0.4808 (tmt) cc_final: 0.3888 (tmm) REVERT: D 35 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8902 (p) REVERT: D 263 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7933 (tpt-90) REVERT: D 305 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8442 (tp) REVERT: D 566 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 574 MET cc_start: 0.7924 (mtm) cc_final: 0.7672 (mtm) REVERT: D 738 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: D 811 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7860 (pt) REVERT: D 1037 MET cc_start: 0.8679 (mmp) cc_final: 0.8390 (mmp) REVERT: D 1410 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8121 (t) REVERT: D 1546 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8985 (pm20) REVERT: D 1646 TRP cc_start: 0.8954 (m-10) cc_final: 0.8532 (m-10) REVERT: D 1654 MET cc_start: 0.9386 (ttp) cc_final: 0.9043 (ptm) REVERT: D 2253 GLU cc_start: 0.8453 (pp20) cc_final: 0.8160 (pp20) REVERT: D 2254 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8593 (tmm) REVERT: D 2410 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7243 (t0) REVERT: D 2411 MET cc_start: 0.4297 (ttp) cc_final: 0.3969 (mtt) REVERT: D 2586 PHE cc_start: 0.9223 (t80) cc_final: 0.8802 (t80) REVERT: D 2692 MET cc_start: 0.4922 (tmt) cc_final: 0.3994 (tmm) REVERT: E 207 MET cc_start: 0.8460 (mtt) cc_final: 0.8150 (mtt) REVERT: E 710 ASP cc_start: 0.7597 (m-30) cc_final: 0.7300 (m-30) REVERT: E 738 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.6528 (m-80) REVERT: E 1147 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8867 (pp) REVERT: E 1191 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8090 (pmm150) REVERT: E 1403 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6885 (p90) REVERT: E 1535 GLN cc_start: 0.7894 (tp40) cc_final: 0.7336 (tp-100) REVERT: E 1654 MET cc_start: 0.9395 (ttp) cc_final: 0.9134 (ptm) REVERT: E 2254 MET cc_start: 0.9092 (tpp) cc_final: 0.8660 (tpp) REVERT: E 2410 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7619 (t0) REVERT: E 2411 MET cc_start: 0.4929 (ttp) cc_final: 0.4428 (mtt) REVERT: E 2586 PHE cc_start: 0.9334 (t80) cc_final: 0.9030 (t80) REVERT: F 317 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7978 (pp) REVERT: F 566 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8271 (tm-30) REVERT: F 738 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6033 (m-80) REVERT: F 1410 VAL cc_start: 0.9017 (p) cc_final: 0.8575 (m) REVERT: F 1498 ARG cc_start: 0.8886 (ttm170) cc_final: 0.8381 (ttp80) REVERT: F 1654 MET cc_start: 0.9259 (ttp) cc_final: 0.9002 (ptm) REVERT: F 2037 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8721 (mp) REVERT: F 2253 GLU cc_start: 0.8190 (pp20) cc_final: 0.7951 (pp20) REVERT: F 2254 MET cc_start: 0.8804 (tmt) cc_final: 0.8085 (tmm) REVERT: F 2411 MET cc_start: 0.5095 (ttp) cc_final: 0.4623 (mtt) REVERT: F 2586 PHE cc_start: 0.9378 (t80) cc_final: 0.8782 (t80) REVERT: F 2666 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8738 (mm) outliers start: 376 outliers final: 245 residues processed: 1144 average time/residue: 0.9854 time to fit residues: 2023.1314 Evaluate side-chains 1030 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 748 time to evaluate : 9.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 610 CYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1546 GLU Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2038 VAL Chi-restraints excluded: chain A residue 2410 ASP Chi-restraints excluded: chain A residue 2421 GLN Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2593 HIS Chi-restraints excluded: chain A residue 2607 VAL Chi-restraints excluded: chain A residue 2666 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2884 LYS Chi-restraints excluded: chain A residue 2903 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 738 PHE Chi-restraints excluded: chain B residue 799 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1160 ASP Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1307 VAL Chi-restraints excluded: chain B residue 1319 VAL Chi-restraints excluded: chain B residue 1331 MET Chi-restraints excluded: chain B residue 1471 VAL Chi-restraints excluded: chain B residue 1508 ASP Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1591 LEU Chi-restraints excluded: chain B residue 1630 LEU Chi-restraints excluded: chain B residue 1666 GLN Chi-restraints excluded: chain B residue 1699 VAL Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2183 TYR Chi-restraints excluded: chain B residue 2367 VAL Chi-restraints excluded: chain B residue 2513 ASP Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2593 HIS Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2894 VAL Chi-restraints excluded: chain B residue 2946 VAL Chi-restraints excluded: chain B residue 3012 VAL Chi-restraints excluded: chain B residue 3051 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 738 PHE Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 893 SER Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1189 LEU Chi-restraints excluded: chain C residue 1265 LEU Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1319 VAL Chi-restraints excluded: chain C residue 1321 VAL Chi-restraints excluded: chain C residue 1331 MET Chi-restraints excluded: chain C residue 1471 VAL Chi-restraints excluded: chain C residue 1526 ILE Chi-restraints excluded: chain C residue 1567 LEU Chi-restraints excluded: chain C residue 1591 LEU Chi-restraints excluded: chain C residue 1629 ASP Chi-restraints excluded: chain C residue 1630 LEU Chi-restraints excluded: chain C residue 1666 GLN Chi-restraints excluded: chain C residue 1699 VAL Chi-restraints excluded: chain C residue 1734 VAL Chi-restraints excluded: chain C residue 2038 VAL Chi-restraints excluded: chain C residue 2194 MET Chi-restraints excluded: chain C residue 2410 ASP Chi-restraints excluded: chain C residue 2513 ASP Chi-restraints excluded: chain C residue 2894 VAL Chi-restraints excluded: chain C residue 2946 VAL Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 738 PHE Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 893 SER Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1160 ASP Chi-restraints excluded: chain D residue 1189 LEU Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1331 MET Chi-restraints excluded: chain D residue 1410 VAL Chi-restraints excluded: chain D residue 1449 VAL Chi-restraints excluded: chain D residue 1526 ILE Chi-restraints excluded: chain D residue 1545 LEU Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1640 LEU Chi-restraints excluded: chain D residue 1695 VAL Chi-restraints excluded: chain D residue 1734 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2073 ASP Chi-restraints excluded: chain D residue 2183 TYR Chi-restraints excluded: chain D residue 2194 MET Chi-restraints excluded: chain D residue 2231 LEU Chi-restraints excluded: chain D residue 2254 MET Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2410 ASP Chi-restraints excluded: chain D residue 2513 ASP Chi-restraints excluded: chain D residue 2607 VAL Chi-restraints excluded: chain D residue 2748 THR Chi-restraints excluded: chain D residue 2894 VAL Chi-restraints excluded: chain D residue 2946 VAL Chi-restraints excluded: chain D residue 3012 VAL Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 712 VAL Chi-restraints excluded: chain E residue 738 PHE Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 893 SER Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 916 ILE Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 1047 VAL Chi-restraints excluded: chain E residue 1147 LEU Chi-restraints excluded: chain E residue 1158 ASP Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1191 ARG Chi-restraints excluded: chain E residue 1243 ILE Chi-restraints excluded: chain E residue 1265 LEU Chi-restraints excluded: chain E residue 1319 VAL Chi-restraints excluded: chain E residue 1331 MET Chi-restraints excluded: chain E residue 1356 MET Chi-restraints excluded: chain E residue 1403 HIS Chi-restraints excluded: chain E residue 1443 ILE Chi-restraints excluded: chain E residue 1445 CYS Chi-restraints excluded: chain E residue 1449 VAL Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1526 ILE Chi-restraints excluded: chain E residue 1545 LEU Chi-restraints excluded: chain E residue 1567 LEU Chi-restraints excluded: chain E residue 1640 LEU Chi-restraints excluded: chain E residue 1695 VAL Chi-restraints excluded: chain E residue 2231 LEU Chi-restraints excluded: chain E residue 2258 LEU Chi-restraints excluded: chain E residue 2410 ASP Chi-restraints excluded: chain E residue 2513 ASP Chi-restraints excluded: chain E residue 2544 VAL Chi-restraints excluded: chain E residue 2607 VAL Chi-restraints excluded: chain E residue 2740 ILE Chi-restraints excluded: chain E residue 2762 LEU Chi-restraints excluded: chain E residue 2946 VAL Chi-restraints excluded: chain E residue 3012 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 712 VAL Chi-restraints excluded: chain F residue 738 PHE Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 777 ASP Chi-restraints excluded: chain F residue 799 PHE Chi-restraints excluded: chain F residue 849 LEU Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 1047 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1158 ASP Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1181 THR Chi-restraints excluded: chain F residue 1189 LEU Chi-restraints excluded: chain F residue 1243 ILE Chi-restraints excluded: chain F residue 1265 LEU Chi-restraints excluded: chain F residue 1266 SER Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1319 VAL Chi-restraints excluded: chain F residue 1331 MET Chi-restraints excluded: chain F residue 1471 VAL Chi-restraints excluded: chain F residue 1567 LEU Chi-restraints excluded: chain F residue 1695 VAL Chi-restraints excluded: chain F residue 1699 VAL Chi-restraints excluded: chain F residue 2037 LEU Chi-restraints excluded: chain F residue 2183 TYR Chi-restraints excluded: chain F residue 2513 ASP Chi-restraints excluded: chain F residue 2544 VAL Chi-restraints excluded: chain F residue 2607 VAL Chi-restraints excluded: chain F residue 2666 LEU Chi-restraints excluded: chain F residue 2762 LEU Chi-restraints excluded: chain F residue 2894 VAL Chi-restraints excluded: chain F residue 2946 VAL Chi-restraints excluded: chain F residue 3012 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1662 random chunks: chunk 991 optimal weight: 0.8980 chunk 639 optimal weight: 3.9990 chunk 956 optimal weight: 4.9990 chunk 482 optimal weight: 9.9990 chunk 314 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 1018 optimal weight: 0.2980 chunk 1091 optimal weight: 1.9990 chunk 791 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 1259 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1403 HIS C1625 GLN ** C2421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2821 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 127536 Z= 0.199 Angle : 0.610 14.225 173910 Z= 0.302 Chirality : 0.044 0.260 20016 Planarity : 0.004 0.128 22932 Dihedral : 4.825 39.597 18080 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.06 % Allowed : 12.79 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.04 % 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: -0.65 (0.07), residues: 16572 helix: 1.13 (0.06), residues: 7488 sheet: -1.28 (0.11), residues: 2124 loop : -1.93 (0.07), residues: 6960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F2605 HIS 0.018 0.001 HIS C 585 PHE 0.035 0.001 PHE F1512 TYR 0.020 0.001 TYR E1404 ARG 0.012 0.000 ARG F 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 392 poor density : 765 time to evaluate : 9.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8312 (mmmt) REVERT: A 738 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: A 811 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7909 (pt) REVERT: A 1147 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8951 (pp) REVERT: A 1230 MET cc_start: 0.8591 (mmm) cc_final: 0.7843 (mmm) REVERT: A 1406 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7669 (t-90) REVERT: A 1498 ARG cc_start: 0.8908 (ttm170) cc_final: 0.8460 (ttp80) REVERT: A 1729 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8468 (mm-30) REVERT: A 2251 GLU cc_start: 0.8785 (pp20) cc_final: 0.8117 (pm20) REVERT: A 2410 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7709 (t0) REVERT: A 2411 MET cc_start: 0.5576 (ttp) cc_final: 0.5107 (mtt) REVERT: A 2586 PHE cc_start: 0.9273 (t80) cc_final: 0.8868 (t80) REVERT: A 2666 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8831 (mm) REVERT: A 2692 MET cc_start: 0.4688 (tmt) cc_final: 0.3380 (tmm) REVERT: B 35 VAL cc_start: 0.9112 (OUTLIER) cc_final: 0.8819 (p) REVERT: B 317 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8267 (pp) REVERT: B 738 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.6311 (m-80) REVERT: B 1410 VAL cc_start: 0.8986 (p) cc_final: 0.8598 (m) REVERT: B 1478 MET cc_start: 0.8264 (ttm) cc_final: 0.8030 (ttp) REVERT: B 1591 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8612 (mp) REVERT: B 1626 GLU cc_start: 0.9178 (tt0) cc_final: 0.8905 (mt-10) REVERT: B 1654 MET cc_start: 0.9237 (ttp) cc_final: 0.8999 (ptm) REVERT: B 2037 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8496 (mp) REVERT: B 2249 ARG cc_start: 0.8669 (ttp-170) cc_final: 0.8197 (ptm160) REVERT: B 2253 GLU cc_start: 0.8235 (pp20) cc_final: 0.8027 (pt0) REVERT: B 2254 MET cc_start: 0.8612 (tmm) cc_final: 0.8310 (tmm) REVERT: B 2367 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8244 (p) REVERT: B 2411 MET cc_start: 0.5419 (ttp) cc_final: 0.4888 (mtt) REVERT: B 2692 MET cc_start: 0.4635 (tmt) cc_final: 0.3725 (tmm) REVERT: C 39 MET cc_start: 0.9055 (mmp) cc_final: 0.8742 (mmm) REVERT: C 273 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8231 (tpp80) REVERT: C 317 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.7921 (pp) REVERT: C 710 ASP cc_start: 0.7742 (m-30) cc_final: 0.7350 (m-30) REVERT: C 738 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: C 811 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7493 (pt) REVERT: C 1037 MET cc_start: 0.8863 (mmp) cc_final: 0.8418 (mmp) REVERT: C 1410 VAL cc_start: 0.9064 (p) cc_final: 0.8702 (m) REVERT: C 1498 ARG cc_start: 0.8828 (ttm170) cc_final: 0.8388 (ttp80) REVERT: C 1591 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8637 (mp) REVERT: C 1629 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8582 (p0) REVERT: C 2252 MET cc_start: 0.9126 (tpt) cc_final: 0.8889 (tpp) REVERT: C 2411 MET cc_start: 0.6194 (ttp) cc_final: 0.5666 (mtt) REVERT: C 2422 MET cc_start: 0.8324 (ttp) cc_final: 0.7900 (ptp) REVERT: C 2586 PHE cc_start: 0.9281 (t80) cc_final: 0.8913 (t80) REVERT: C 2692 MET cc_start: 0.4739 (tmt) cc_final: 0.3838 (tmm) REVERT: D 35 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8882 (p) REVERT: D 263 ARG cc_start: 0.8261 (tpp80) cc_final: 0.7983 (tpt-90) REVERT: D 305 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8461 (tp) REVERT: D 566 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8189 (tm-30) REVERT: D 574 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7657 (mtm) REVERT: D 738 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: D 811 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7871 (pt) REVERT: D 1037 MET cc_start: 0.8732 (mmp) cc_final: 0.8413 (mmp) REVERT: D 1410 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8223 (t) REVERT: D 1646 TRP cc_start: 0.8938 (m-10) cc_final: 0.8637 (m-10) REVERT: D 1654 MET cc_start: 0.9390 (ttp) cc_final: 0.9055 (ptp) REVERT: D 2253 GLU cc_start: 0.8446 (pp20) cc_final: 0.8144 (pp20) REVERT: D 2254 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8589 (tmm) REVERT: D 2410 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7250 (t0) REVERT: D 2411 MET cc_start: 0.4345 (ttp) cc_final: 0.3982 (mtt) REVERT: D 2586 PHE cc_start: 0.9261 (t80) cc_final: 0.8858 (t80) REVERT: D 2692 MET cc_start: 0.4825 (tmt) cc_final: 0.3972 (tmm) REVERT: E 207 MET cc_start: 0.8456 (mtt) cc_final: 0.8182 (mtt) REVERT: E 305 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8634 (tp) REVERT: E 710 ASP cc_start: 0.7662 (m-30) cc_final: 0.7336 (m-30) REVERT: E 738 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.6773 (m-80) REVERT: E 1147 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8866 (pp) REVERT: E 1230 MET cc_start: 0.9046 (mmm) cc_final: 0.8360 (mmm) REVERT: E 1406 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7227 (t-90) REVERT: E 1535 GLN cc_start: 0.7911 (tp40) cc_final: 0.7335 (tp-100) REVERT: E 1654 MET cc_start: 0.9406 (ttp) cc_final: 0.9153 (ptm) REVERT: E 2254 MET cc_start: 0.9083 (tpp) cc_final: 0.8707 (tpp) REVERT: E 2410 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7645 (t0) REVERT: E 2411 MET cc_start: 0.4966 (ttp) cc_final: 0.4446 (mtt) REVERT: E 2586 PHE cc_start: 0.9319 (t80) cc_final: 0.9018 (t80) REVERT: F 317 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8009 (pp) REVERT: F 566 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8260 (tm-30) REVERT: F 738 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6264 (m-80) REVERT: F 1410 VAL cc_start: 0.9034 (p) cc_final: 0.8578 (m) REVERT: F 1498 ARG cc_start: 0.8903 (ttm170) cc_final: 0.8359 (ttp80) REVERT: F 1654 MET cc_start: 0.9235 (ttp) cc_final: 0.8992 (ptm) REVERT: F 2037 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8758 (mp) REVERT: F 2253 GLU cc_start: 0.8223 (pp20) cc_final: 0.7972 (pp20) REVERT: F 2254 MET cc_start: 0.8818 (tmt) cc_final: 0.8036 (tpp) REVERT: F 2411 MET cc_start: 0.5103 (ttp) cc_final: 0.4612 (mtt) REVERT: F 2586 PHE cc_start: 0.9391 (t80) cc_final: 0.9026 (t80) REVERT: F 2666 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8729 (mm) outliers start: 392 outliers final: 281 residues processed: 1091 average time/residue: 0.9494 time to fit residues: 1874.1214 Evaluate side-chains 1053 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 737 time to evaluate : 9.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1403 HIS Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2038 VAL Chi-restraints excluded: chain A residue 2224 ASP Chi-restraints excluded: chain A residue 2256 VAL Chi-restraints excluded: chain A residue 2410 ASP Chi-restraints excluded: chain A residue 2421 GLN Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2593 HIS Chi-restraints excluded: chain A residue 2607 VAL Chi-restraints excluded: chain A residue 2658 MET Chi-restraints excluded: chain A residue 2666 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2884 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 738 PHE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 799 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1160 ASP Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1307 VAL Chi-restraints excluded: chain B residue 1331 MET Chi-restraints excluded: chain B residue 1403 HIS Chi-restraints excluded: chain B residue 1471 VAL Chi-restraints excluded: chain B residue 1508 ASP Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1591 LEU Chi-restraints excluded: chain B residue 1666 GLN Chi-restraints excluded: chain B residue 1695 VAL Chi-restraints excluded: chain B residue 1699 VAL Chi-restraints excluded: chain B residue 1734 VAL Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2183 TYR Chi-restraints excluded: chain B residue 2367 VAL Chi-restraints excluded: chain B residue 2513 ASP Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2894 VAL Chi-restraints excluded: chain B residue 2946 VAL Chi-restraints excluded: chain B residue 3012 VAL Chi-restraints excluded: chain B residue 3051 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 738 PHE Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 893 SER Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1189 LEU Chi-restraints excluded: chain C residue 1265 LEU Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1319 VAL Chi-restraints excluded: chain C residue 1321 VAL Chi-restraints excluded: chain C residue 1331 MET Chi-restraints excluded: chain C residue 1395 THR Chi-restraints excluded: chain C residue 1403 HIS Chi-restraints excluded: chain C residue 1471 VAL Chi-restraints excluded: chain C residue 1526 ILE Chi-restraints excluded: chain C residue 1567 LEU Chi-restraints excluded: chain C residue 1591 LEU Chi-restraints excluded: chain C residue 1629 ASP Chi-restraints excluded: chain C residue 1630 LEU Chi-restraints excluded: chain C residue 1666 GLN Chi-restraints excluded: chain C residue 1699 VAL Chi-restraints excluded: chain C residue 1734 VAL Chi-restraints excluded: chain C residue 2038 VAL Chi-restraints excluded: chain C residue 2194 MET Chi-restraints excluded: chain C residue 2224 ASP Chi-restraints excluded: chain C residue 2475 ILE Chi-restraints excluded: chain C residue 2513 ASP Chi-restraints excluded: chain C residue 2748 THR Chi-restraints excluded: chain C residue 2894 VAL Chi-restraints excluded: chain C residue 2946 VAL Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3051 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 738 PHE Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 893 SER Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1160 ASP Chi-restraints excluded: chain D residue 1189 LEU Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1403 HIS Chi-restraints excluded: chain D residue 1410 VAL Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1449 VAL Chi-restraints excluded: chain D residue 1526 ILE Chi-restraints excluded: chain D residue 1545 LEU Chi-restraints excluded: chain D residue 1640 LEU Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1734 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2073 ASP Chi-restraints excluded: chain D residue 2183 TYR Chi-restraints excluded: chain D residue 2194 MET Chi-restraints excluded: chain D residue 2224 ASP Chi-restraints excluded: chain D residue 2231 LEU Chi-restraints excluded: chain D residue 2254 MET Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2410 ASP Chi-restraints excluded: chain D residue 2475 ILE Chi-restraints excluded: chain D residue 2513 ASP Chi-restraints excluded: chain D residue 2607 VAL Chi-restraints excluded: chain D residue 2748 THR Chi-restraints excluded: chain D residue 2833 LEU Chi-restraints excluded: chain D residue 2894 VAL Chi-restraints excluded: chain D residue 2946 VAL Chi-restraints excluded: chain D residue 3012 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 712 VAL Chi-restraints excluded: chain E residue 738 PHE Chi-restraints excluded: chain E residue 777 ASP Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 893 SER Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 916 ILE Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 1047 VAL Chi-restraints excluded: chain E residue 1147 LEU Chi-restraints excluded: chain E residue 1158 ASP Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1243 ILE Chi-restraints excluded: chain E residue 1265 LEU Chi-restraints excluded: chain E residue 1331 MET Chi-restraints excluded: chain E residue 1356 MET Chi-restraints excluded: chain E residue 1403 HIS Chi-restraints excluded: chain E residue 1406 HIS Chi-restraints excluded: chain E residue 1443 ILE Chi-restraints excluded: chain E residue 1445 CYS Chi-restraints excluded: chain E residue 1449 VAL Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1526 ILE Chi-restraints excluded: chain E residue 1545 LEU Chi-restraints excluded: chain E residue 1567 LEU Chi-restraints excluded: chain E residue 1640 LEU Chi-restraints excluded: chain E residue 1695 VAL Chi-restraints excluded: chain E residue 2194 MET Chi-restraints excluded: chain E residue 2224 ASP Chi-restraints excluded: chain E residue 2231 LEU Chi-restraints excluded: chain E residue 2258 LEU Chi-restraints excluded: chain E residue 2410 ASP Chi-restraints excluded: chain E residue 2421 GLN Chi-restraints excluded: chain E residue 2513 ASP Chi-restraints excluded: chain E residue 2544 VAL Chi-restraints excluded: chain E residue 2607 VAL Chi-restraints excluded: chain E residue 2740 ILE Chi-restraints excluded: chain E residue 2762 LEU Chi-restraints excluded: chain E residue 2884 LYS Chi-restraints excluded: chain E residue 2946 VAL Chi-restraints excluded: chain E residue 3012 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 712 VAL Chi-restraints excluded: chain F residue 738 PHE Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 777 ASP Chi-restraints excluded: chain F residue 799 PHE Chi-restraints excluded: chain F residue 849 LEU Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 893 SER Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 934 LEU Chi-restraints excluded: chain F residue 1039 THR Chi-restraints excluded: chain F residue 1047 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1158 ASP Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1181 THR Chi-restraints excluded: chain F residue 1189 LEU Chi-restraints excluded: chain F residue 1243 ILE Chi-restraints excluded: chain F residue 1265 LEU Chi-restraints excluded: chain F residue 1266 SER Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1319 VAL Chi-restraints excluded: chain F residue 1331 MET Chi-restraints excluded: chain F residue 1471 VAL Chi-restraints excluded: chain F residue 1508 ASP Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1567 LEU Chi-restraints excluded: chain F residue 1695 VAL Chi-restraints excluded: chain F residue 1699 VAL Chi-restraints excluded: chain F residue 1713 LEU Chi-restraints excluded: chain F residue 2037 LEU Chi-restraints excluded: chain F residue 2183 TYR Chi-restraints excluded: chain F residue 2513 ASP Chi-restraints excluded: chain F residue 2544 VAL Chi-restraints excluded: chain F residue 2666 LEU Chi-restraints excluded: chain F residue 2748 THR Chi-restraints excluded: chain F residue 2762 LEU Chi-restraints excluded: chain F residue 2894 VAL Chi-restraints excluded: chain F residue 2946 VAL Chi-restraints excluded: chain F residue 3012 VAL Chi-restraints excluded: chain F residue 3051 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1662 random chunks: chunk 1457 optimal weight: 3.9990 chunk 1534 optimal weight: 3.9990 chunk 1400 optimal weight: 2.9990 chunk 1492 optimal weight: 0.9980 chunk 898 optimal weight: 7.9990 chunk 650 optimal weight: 8.9990 chunk 1172 optimal weight: 2.9990 chunk 458 optimal weight: 1.9990 chunk 1348 optimal weight: 20.0000 chunk 1411 optimal weight: 8.9990 chunk 1487 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1403 HIS C1625 GLN ** C2421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1403 HIS ** F1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2012 ASN ** F2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3033 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 127536 Z= 0.219 Angle : 0.618 14.143 173910 Z= 0.307 Chirality : 0.044 0.281 20016 Planarity : 0.004 0.078 22932 Dihedral : 4.843 40.772 18080 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.86 % Allowed : 13.03 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.04 % 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: -0.61 (0.07), residues: 16572 helix: 1.15 (0.06), residues: 7452 sheet: -1.24 (0.11), residues: 2124 loop : -1.89 (0.07), residues: 6996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E2456 HIS 0.017 0.001 HIS C1403 PHE 0.032 0.001 PHE A1587 TYR 0.044 0.001 TYR C1404 ARG 0.011 0.000 ARG A2419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 367 poor density : 752 time to evaluate : 9.020 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 570 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8301 (mmmt) REVERT: A 738 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: A 811 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7923 (pt) REVERT: A 1147 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8902 (pp) REVERT: A 1230 MET cc_start: 0.8684 (mmm) cc_final: 0.7944 (mmm) REVERT: A 1406 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7672 (t-90) REVERT: A 1498 ARG cc_start: 0.8924 (ttm170) cc_final: 0.8505 (ttp80) REVERT: A 1729 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8464 (mm-30) REVERT: A 2410 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7892 (t0) REVERT: A 2411 MET cc_start: 0.5463 (ttp) cc_final: 0.5064 (mtt) REVERT: A 2586 PHE cc_start: 0.9278 (t80) cc_final: 0.8857 (t80) REVERT: A 2666 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8823 (mm) REVERT: A 2692 MET cc_start: 0.4633 (tmt) cc_final: 0.3468 (tmm) REVERT: B 317 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8267 (pp) REVERT: B 738 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.6350 (m-80) REVERT: B 1410 VAL cc_start: 0.9002 (p) cc_final: 0.8621 (m) REVERT: B 1478 MET cc_start: 0.8274 (ttm) cc_final: 0.8024 (ttp) REVERT: B 1591 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8640 (mp) REVERT: B 1626 GLU cc_start: 0.9196 (tt0) cc_final: 0.8906 (mt-10) REVERT: B 1654 MET cc_start: 0.9230 (ttp) cc_final: 0.9011 (ptm) REVERT: B 2037 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8486 (mp) REVERT: B 2249 ARG cc_start: 0.8659 (ttp-170) cc_final: 0.8406 (ptm160) REVERT: B 2254 MET cc_start: 0.8591 (tmm) cc_final: 0.8328 (tmm) REVERT: B 2367 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8250 (p) REVERT: B 2411 MET cc_start: 0.5428 (ttp) cc_final: 0.4883 (mtt) REVERT: C 39 MET cc_start: 0.9052 (mmp) cc_final: 0.8730 (mmm) REVERT: C 273 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.6740 (tpp80) REVERT: C 317 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7910 (pp) REVERT: C 710 ASP cc_start: 0.7771 (m-30) cc_final: 0.7382 (m-30) REVERT: C 738 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: C 1410 VAL cc_start: 0.9066 (p) cc_final: 0.8710 (m) REVERT: C 1498 ARG cc_start: 0.8831 (ttm170) cc_final: 0.8408 (ttp80) REVERT: C 1543 ARG cc_start: 0.9161 (mmm-85) cc_final: 0.8837 (mmm160) REVERT: C 1546 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8835 (pm20) REVERT: C 1591 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8641 (mp) REVERT: C 1629 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8591 (p0) REVERT: C 2252 MET cc_start: 0.9141 (tpt) cc_final: 0.8895 (tpp) REVERT: C 2410 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.7756 (t0) REVERT: C 2411 MET cc_start: 0.6126 (ttp) cc_final: 0.5583 (mtt) REVERT: C 2586 PHE cc_start: 0.9280 (t80) cc_final: 0.8912 (t80) REVERT: C 2692 MET cc_start: 0.4752 (tmt) cc_final: 0.3756 (tmt) REVERT: D 35 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8930 (p) REVERT: D 305 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8459 (tp) REVERT: D 566 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8172 (tm-30) REVERT: D 738 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: D 811 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7887 (pt) REVERT: D 1037 MET cc_start: 0.8742 (mmp) cc_final: 0.8420 (mmp) REVERT: D 1410 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8310 (t) REVERT: D 1646 TRP cc_start: 0.8957 (m-10) cc_final: 0.8634 (m-10) REVERT: D 1654 MET cc_start: 0.9391 (ttp) cc_final: 0.9044 (ptp) REVERT: D 2253 GLU cc_start: 0.8449 (pp20) cc_final: 0.8145 (pp20) REVERT: D 2254 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8580 (tmm) REVERT: D 2410 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7305 (t0) REVERT: D 2411 MET cc_start: 0.4428 (ttp) cc_final: 0.4154 (mtt) REVERT: D 2586 PHE cc_start: 0.9311 (t80) cc_final: 0.8878 (t80) REVERT: D 2692 MET cc_start: 0.4947 (tmt) cc_final: 0.3878 (tmm) REVERT: E 207 MET cc_start: 0.8466 (mtt) cc_final: 0.8180 (mtt) REVERT: E 305 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8587 (tp) REVERT: E 738 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.6896 (m-80) REVERT: E 900 MET cc_start: 0.8479 (mmm) cc_final: 0.8232 (mtt) REVERT: E 1147 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8878 (pp) REVERT: E 1230 MET cc_start: 0.9066 (mmm) cc_final: 0.8437 (mmm) REVERT: E 1406 HIS cc_start: 0.8082 (OUTLIER) cc_final: 0.7280 (t-90) REVERT: E 1535 GLN cc_start: 0.7892 (tp40) cc_final: 0.7352 (tp-100) REVERT: E 1654 MET cc_start: 0.9403 (ttp) cc_final: 0.9153 (ptm) REVERT: E 2254 MET cc_start: 0.9086 (tpp) cc_final: 0.8689 (tpp) REVERT: E 2410 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7646 (t0) REVERT: E 2411 MET cc_start: 0.4813 (ttp) cc_final: 0.4308 (mtt) REVERT: E 2586 PHE cc_start: 0.9322 (t80) cc_final: 0.9009 (t80) REVERT: F 317 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8040 (pp) REVERT: F 566 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8284 (tm-30) REVERT: F 738 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6302 (m-80) REVERT: F 1410 VAL cc_start: 0.9043 (p) cc_final: 0.8576 (m) REVERT: F 1498 ARG cc_start: 0.8906 (ttm170) cc_final: 0.8383 (ttp80) REVERT: F 1654 MET cc_start: 0.9224 (ttp) cc_final: 0.8997 (ptm) REVERT: F 2037 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8723 (mp) REVERT: F 2253 GLU cc_start: 0.8234 (pp20) cc_final: 0.7927 (pp20) REVERT: F 2254 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8089 (tpp) REVERT: F 2411 MET cc_start: 0.5119 (ttp) cc_final: 0.4680 (mtt) REVERT: F 2586 PHE cc_start: 0.9369 (t80) cc_final: 0.8993 (t80) REVERT: F 2666 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8753 (mm) outliers start: 367 outliers final: 292 residues processed: 1054 average time/residue: 1.0118 time to fit residues: 1923.3242 Evaluate side-chains 1052 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 725 time to evaluate : 9.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1403 HIS Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2038 VAL Chi-restraints excluded: chain A residue 2224 ASP Chi-restraints excluded: chain A residue 2256 VAL Chi-restraints excluded: chain A residue 2410 ASP Chi-restraints excluded: chain A residue 2421 GLN Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2593 HIS Chi-restraints excluded: chain A residue 2666 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2859 ILE Chi-restraints excluded: chain A residue 2884 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 738 PHE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 799 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1160 ASP Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1307 VAL Chi-restraints excluded: chain B residue 1331 MET Chi-restraints excluded: chain B residue 1471 VAL Chi-restraints excluded: chain B residue 1508 ASP Chi-restraints excluded: chain B residue 1546 GLU Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1591 LEU Chi-restraints excluded: chain B residue 1666 GLN Chi-restraints excluded: chain B residue 1695 VAL Chi-restraints excluded: chain B residue 1699 VAL Chi-restraints excluded: chain B residue 1734 VAL Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2183 TYR Chi-restraints excluded: chain B residue 2224 ASP Chi-restraints excluded: chain B residue 2275 ARG Chi-restraints excluded: chain B residue 2367 VAL Chi-restraints excluded: chain B residue 2513 ASP Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2859 ILE Chi-restraints excluded: chain B residue 2894 VAL Chi-restraints excluded: chain B residue 2946 VAL Chi-restraints excluded: chain B residue 3012 VAL Chi-restraints excluded: chain B residue 3051 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 738 PHE Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 893 SER Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1189 LEU Chi-restraints excluded: chain C residue 1243 ILE Chi-restraints excluded: chain C residue 1265 LEU Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1319 VAL Chi-restraints excluded: chain C residue 1321 VAL Chi-restraints excluded: chain C residue 1331 MET Chi-restraints excluded: chain C residue 1395 THR Chi-restraints excluded: chain C residue 1402 VAL Chi-restraints excluded: chain C residue 1403 HIS Chi-restraints excluded: chain C residue 1471 VAL Chi-restraints excluded: chain C residue 1526 ILE Chi-restraints excluded: chain C residue 1546 GLU Chi-restraints excluded: chain C residue 1567 LEU Chi-restraints excluded: chain C residue 1591 LEU Chi-restraints excluded: chain C residue 1629 ASP Chi-restraints excluded: chain C residue 1630 LEU Chi-restraints excluded: chain C residue 1666 GLN Chi-restraints excluded: chain C residue 1699 VAL Chi-restraints excluded: chain C residue 1734 VAL Chi-restraints excluded: chain C residue 2038 VAL Chi-restraints excluded: chain C residue 2194 MET Chi-restraints excluded: chain C residue 2224 ASP Chi-restraints excluded: chain C residue 2410 ASP Chi-restraints excluded: chain C residue 2475 ILE Chi-restraints excluded: chain C residue 2513 ASP Chi-restraints excluded: chain C residue 2748 THR Chi-restraints excluded: chain C residue 2894 VAL Chi-restraints excluded: chain C residue 2946 VAL Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3051 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 738 PHE Chi-restraints excluded: chain D residue 777 ASP Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 846 CYS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 893 SER Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1140 LEU Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1160 ASP Chi-restraints excluded: chain D residue 1189 LEU Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1403 HIS Chi-restraints excluded: chain D residue 1410 VAL Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1449 VAL Chi-restraints excluded: chain D residue 1503 ASP Chi-restraints excluded: chain D residue 1526 ILE Chi-restraints excluded: chain D residue 1545 LEU Chi-restraints excluded: chain D residue 1640 LEU Chi-restraints excluded: chain D residue 1695 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1734 VAL Chi-restraints excluded: chain D residue 2183 TYR Chi-restraints excluded: chain D residue 2194 MET Chi-restraints excluded: chain D residue 2224 ASP Chi-restraints excluded: chain D residue 2231 LEU Chi-restraints excluded: chain D residue 2254 MET Chi-restraints excluded: chain D residue 2256 VAL Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2410 ASP Chi-restraints excluded: chain D residue 2475 ILE Chi-restraints excluded: chain D residue 2513 ASP Chi-restraints excluded: chain D residue 2607 VAL Chi-restraints excluded: chain D residue 2748 THR Chi-restraints excluded: chain D residue 2833 LEU Chi-restraints excluded: chain D residue 2859 ILE Chi-restraints excluded: chain D residue 2894 VAL Chi-restraints excluded: chain D residue 2946 VAL Chi-restraints excluded: chain D residue 3012 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 712 VAL Chi-restraints excluded: chain E residue 738 PHE Chi-restraints excluded: chain E residue 745 THR Chi-restraints excluded: chain E residue 777 ASP Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 893 SER Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 916 ILE Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 1047 VAL Chi-restraints excluded: chain E residue 1147 LEU Chi-restraints excluded: chain E residue 1158 ASP Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1243 ILE Chi-restraints excluded: chain E residue 1265 LEU Chi-restraints excluded: chain E residue 1331 MET Chi-restraints excluded: chain E residue 1356 MET Chi-restraints excluded: chain E residue 1406 HIS Chi-restraints excluded: chain E residue 1443 ILE Chi-restraints excluded: chain E residue 1445 CYS Chi-restraints excluded: chain E residue 1447 HIS Chi-restraints excluded: chain E residue 1449 VAL Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1526 ILE Chi-restraints excluded: chain E residue 1545 LEU Chi-restraints excluded: chain E residue 1546 GLU Chi-restraints excluded: chain E residue 1567 LEU Chi-restraints excluded: chain E residue 1640 LEU Chi-restraints excluded: chain E residue 2194 MET Chi-restraints excluded: chain E residue 2224 ASP Chi-restraints excluded: chain E residue 2231 LEU Chi-restraints excluded: chain E residue 2258 LEU Chi-restraints excluded: chain E residue 2410 ASP Chi-restraints excluded: chain E residue 2421 GLN Chi-restraints excluded: chain E residue 2513 ASP Chi-restraints excluded: chain E residue 2544 VAL Chi-restraints excluded: chain E residue 2607 VAL Chi-restraints excluded: chain E residue 2740 ILE Chi-restraints excluded: chain E residue 2762 LEU Chi-restraints excluded: chain E residue 2859 ILE Chi-restraints excluded: chain E residue 2884 LYS Chi-restraints excluded: chain E residue 2946 VAL Chi-restraints excluded: chain E residue 3012 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 712 VAL Chi-restraints excluded: chain F residue 738 PHE Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain F residue 777 ASP Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 799 PHE Chi-restraints excluded: chain F residue 849 LEU Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 893 SER Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 1039 THR Chi-restraints excluded: chain F residue 1047 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1158 ASP Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1181 THR Chi-restraints excluded: chain F residue 1189 LEU Chi-restraints excluded: chain F residue 1243 ILE Chi-restraints excluded: chain F residue 1265 LEU Chi-restraints excluded: chain F residue 1266 SER Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1319 VAL Chi-restraints excluded: chain F residue 1331 MET Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1471 VAL Chi-restraints excluded: chain F residue 1508 ASP Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1567 LEU Chi-restraints excluded: chain F residue 1695 VAL Chi-restraints excluded: chain F residue 1699 VAL Chi-restraints excluded: chain F residue 1713 LEU Chi-restraints excluded: chain F residue 2037 LEU Chi-restraints excluded: chain F residue 2038 VAL Chi-restraints excluded: chain F residue 2183 TYR Chi-restraints excluded: chain F residue 2224 ASP Chi-restraints excluded: chain F residue 2254 MET Chi-restraints excluded: chain F residue 2513 ASP Chi-restraints excluded: chain F residue 2544 VAL Chi-restraints excluded: chain F residue 2666 LEU Chi-restraints excluded: chain F residue 2748 THR Chi-restraints excluded: chain F residue 2762 LEU Chi-restraints excluded: chain F residue 2859 ILE Chi-restraints excluded: chain F residue 2894 VAL Chi-restraints excluded: chain F residue 2946 VAL Chi-restraints excluded: chain F residue 3012 VAL Chi-restraints excluded: chain F residue 3051 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1662 random chunks: chunk 980 optimal weight: 0.9980 chunk 1578 optimal weight: 5.9990 chunk 963 optimal weight: 10.0000 chunk 748 optimal weight: 6.9990 chunk 1097 optimal weight: 1.9990 chunk 1655 optimal weight: 3.9990 chunk 1523 optimal weight: 8.9990 chunk 1318 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 1018 optimal weight: 0.9980 chunk 808 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1576 HIS ** B2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3033 GLN ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3033 GLN ** F2421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3033 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 127536 Z= 0.248 Angle : 0.635 14.605 173910 Z= 0.316 Chirality : 0.044 0.301 20016 Planarity : 0.004 0.072 22932 Dihedral : 4.904 42.415 18080 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.71 % Allowed : 13.19 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.05 % 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: -0.62 (0.07), residues: 16572 helix: 1.14 (0.06), residues: 7446 sheet: -1.32 (0.11), residues: 2172 loop : -1.87 (0.07), residues: 6954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E2326 HIS 0.011 0.001 HIS C1403 PHE 0.030 0.001 PHE F1512 TYR 0.036 0.001 TYR C1404 ARG 0.017 0.000 ARG D2419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33144 Ramachandran restraints generated. 16572 Oldfield, 0 Emsley, 16572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 724 time to evaluate : 9.985 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: A 570 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8313 (mmmt) REVERT: A 738 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: A 811 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7920 (pt) REVERT: A 1147 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8894 (pp) REVERT: A 1230 MET cc_start: 0.8728 (mmm) cc_final: 0.8023 (mmm) REVERT: A 1406 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.7637 (t-90) REVERT: A 1498 ARG cc_start: 0.8930 (ttm170) cc_final: 0.8534 (ttp80) REVERT: A 1729 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8453 (mm-30) REVERT: A 2410 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7701 (t0) REVERT: A 2411 MET cc_start: 0.5602 (ttp) cc_final: 0.5115 (mtt) REVERT: A 2586 PHE cc_start: 0.9290 (t80) cc_final: 0.8877 (t80) REVERT: A 2666 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8861 (mm) REVERT: A 2692 MET cc_start: 0.4571 (tmt) cc_final: 0.3356 (tmm) REVERT: B 317 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8236 (pp) REVERT: B 738 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.6410 (m-80) REVERT: B 1410 VAL cc_start: 0.8986 (p) cc_final: 0.8571 (m) REVERT: B 1478 MET cc_start: 0.8331 (ttm) cc_final: 0.8099 (ttp) REVERT: B 1591 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8659 (mp) REVERT: B 1626 GLU cc_start: 0.9198 (tt0) cc_final: 0.8893 (mt-10) REVERT: B 1654 MET cc_start: 0.9239 (ttp) cc_final: 0.9019 (ptm) REVERT: B 2037 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8508 (mp) REVERT: B 2254 MET cc_start: 0.8562 (tmm) cc_final: 0.8300 (tmm) REVERT: B 2367 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8290 (p) REVERT: B 2411 MET cc_start: 0.5433 (ttp) cc_final: 0.4885 (mtt) REVERT: C 39 MET cc_start: 0.9061 (mmp) cc_final: 0.8759 (mmm) REVERT: C 273 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.6709 (tpp80) REVERT: C 317 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7925 (pp) REVERT: C 710 ASP cc_start: 0.7781 (m-30) cc_final: 0.7395 (m-30) REVERT: C 738 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: C 1037 MET cc_start: 0.8571 (mmp) cc_final: 0.8053 (mmp) REVERT: C 1410 VAL cc_start: 0.9092 (p) cc_final: 0.8740 (m) REVERT: C 1498 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8443 (ttp80) REVERT: C 1543 ARG cc_start: 0.9163 (mmm-85) cc_final: 0.8837 (mmm160) REVERT: C 1546 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8842 (pm20) REVERT: C 1591 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8627 (mp) REVERT: C 1629 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8605 (p0) REVERT: C 2252 MET cc_start: 0.9225 (tpt) cc_final: 0.8984 (tpp) REVERT: C 2411 MET cc_start: 0.6004 (ttp) cc_final: 0.5645 (mtt) REVERT: C 2422 MET cc_start: 0.8331 (ttp) cc_final: 0.7922 (ptp) REVERT: C 2586 PHE cc_start: 0.9277 (t80) cc_final: 0.8913 (t80) REVERT: D 207 MET cc_start: 0.8109 (mtt) cc_final: 0.7763 (mtt) REVERT: D 263 ARG cc_start: 0.7893 (tpt-90) cc_final: 0.7217 (tpt170) REVERT: D 267 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7605 (mt-10) REVERT: D 305 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8463 (tp) REVERT: D 566 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8175 (tm-30) REVERT: D 738 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: D 811 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7854 (pt) REVERT: D 1037 MET cc_start: 0.8769 (mmp) cc_final: 0.8449 (mmp) REVERT: D 1410 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8349 (t) REVERT: D 1654 MET cc_start: 0.9389 (ttp) cc_final: 0.9174 (ptm) REVERT: D 2253 GLU cc_start: 0.8448 (pp20) cc_final: 0.8144 (pp20) REVERT: D 2254 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8583 (tmm) REVERT: D 2410 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7257 (t0) REVERT: D 2411 MET cc_start: 0.4693 (ttp) cc_final: 0.4110 (mtt) REVERT: D 2586 PHE cc_start: 0.9313 (t80) cc_final: 0.8876 (t80) REVERT: D 2692 MET cc_start: 0.4974 (tmt) cc_final: 0.4069 (tmm) REVERT: E 207 MET cc_start: 0.8484 (mtt) cc_final: 0.8195 (mtt) REVERT: E 305 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8592 (tp) REVERT: E 738 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7033 (m-80) REVERT: E 1147 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8874 (pp) REVERT: E 1184 GLU cc_start: 0.8503 (pm20) cc_final: 0.8236 (pm20) REVERT: E 1230 MET cc_start: 0.9091 (mmm) cc_final: 0.8469 (mmm) REVERT: E 1406 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7374 (t-90) REVERT: E 1535 GLN cc_start: 0.7968 (tp40) cc_final: 0.7412 (tp-100) REVERT: E 1654 MET cc_start: 0.9392 (ttp) cc_final: 0.9138 (ptm) REVERT: E 2254 MET cc_start: 0.9109 (tpp) cc_final: 0.8690 (tpp) REVERT: E 2410 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7650 (t0) REVERT: E 2411 MET cc_start: 0.4886 (ttp) cc_final: 0.4343 (mtt) REVERT: E 2586 PHE cc_start: 0.9331 (t80) cc_final: 0.9015 (t80) REVERT: E 2692 MET cc_start: 0.4276 (tmt) cc_final: 0.3556 (tmt) REVERT: F 270 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8078 (tm-30) REVERT: F 317 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8056 (pp) REVERT: F 566 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8268 (tm-30) REVERT: F 738 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.6369 (m-80) REVERT: F 1498 ARG cc_start: 0.8928 (ttm170) cc_final: 0.8411 (ttp80) REVERT: F 1654 MET cc_start: 0.9215 (ttp) cc_final: 0.8992 (ptm) REVERT: F 2037 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8544 (mp) REVERT: F 2253 GLU cc_start: 0.8275 (pp20) cc_final: 0.7985 (pp20) REVERT: F 2254 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8253 (tpp) REVERT: F 2411 MET cc_start: 0.5119 (ttp) cc_final: 0.4672 (mtt) REVERT: F 2586 PHE cc_start: 0.9335 (t80) cc_final: 0.8994 (t80) REVERT: F 2666 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8751 (mm) outliers start: 347 outliers final: 291 residues processed: 1011 average time/residue: 0.9905 time to fit residues: 1813.5271 Evaluate side-chains 1025 residues out of total 12828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 701 time to evaluate : 10.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 610 CYS Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1147 LEU Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1403 HIS Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1447 HIS Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2038 VAL Chi-restraints excluded: chain A residue 2224 ASP Chi-restraints excluded: chain A residue 2256 VAL Chi-restraints excluded: chain A residue 2410 ASP Chi-restraints excluded: chain A residue 2421 GLN Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2593 HIS Chi-restraints excluded: chain A residue 2658 MET Chi-restraints excluded: chain A residue 2666 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2833 LEU Chi-restraints excluded: chain A residue 2859 ILE Chi-restraints excluded: chain A residue 2884 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 738 PHE Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 799 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 1039 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1160 ASP Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1307 VAL Chi-restraints excluded: chain B residue 1331 MET Chi-restraints excluded: chain B residue 1413 LEU Chi-restraints excluded: chain B residue 1471 VAL Chi-restraints excluded: chain B residue 1508 ASP Chi-restraints excluded: chain B residue 1546 GLU Chi-restraints excluded: chain B residue 1567 LEU Chi-restraints excluded: chain B residue 1591 LEU Chi-restraints excluded: chain B residue 1630 LEU Chi-restraints excluded: chain B residue 1666 GLN Chi-restraints excluded: chain B residue 1695 VAL Chi-restraints excluded: chain B residue 1699 VAL Chi-restraints excluded: chain B residue 1734 VAL Chi-restraints excluded: chain B residue 2037 LEU Chi-restraints excluded: chain B residue 2183 TYR Chi-restraints excluded: chain B residue 2224 ASP Chi-restraints excluded: chain B residue 2275 ARG Chi-restraints excluded: chain B residue 2367 VAL Chi-restraints excluded: chain B residue 2513 ASP Chi-restraints excluded: chain B residue 2544 VAL Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2859 ILE Chi-restraints excluded: chain B residue 2894 VAL Chi-restraints excluded: chain B residue 2946 VAL Chi-restraints excluded: chain B residue 3012 VAL Chi-restraints excluded: chain B residue 3051 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 738 PHE Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 893 SER Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1189 LEU Chi-restraints excluded: chain C residue 1243 ILE Chi-restraints excluded: chain C residue 1265 LEU Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1319 VAL Chi-restraints excluded: chain C residue 1321 VAL Chi-restraints excluded: chain C residue 1331 MET Chi-restraints excluded: chain C residue 1526 ILE Chi-restraints excluded: chain C residue 1546 GLU Chi-restraints excluded: chain C residue 1567 LEU Chi-restraints excluded: chain C residue 1591 LEU Chi-restraints excluded: chain C residue 1629 ASP Chi-restraints excluded: chain C residue 1630 LEU Chi-restraints excluded: chain C residue 1666 GLN Chi-restraints excluded: chain C residue 1699 VAL Chi-restraints excluded: chain C residue 1734 VAL Chi-restraints excluded: chain C residue 2038 VAL Chi-restraints excluded: chain C residue 2194 MET Chi-restraints excluded: chain C residue 2224 ASP Chi-restraints excluded: chain C residue 2268 LEU Chi-restraints excluded: chain C residue 2475 ILE Chi-restraints excluded: chain C residue 2513 ASP Chi-restraints excluded: chain C residue 2748 THR Chi-restraints excluded: chain C residue 2894 VAL Chi-restraints excluded: chain C residue 2946 VAL Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3051 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 738 PHE Chi-restraints excluded: chain D residue 777 ASP Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 846 CYS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 VAL Chi-restraints excluded: chain D residue 893 SER Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1160 ASP Chi-restraints excluded: chain D residue 1189 LEU Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1403 HIS Chi-restraints excluded: chain D residue 1410 VAL Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1449 VAL Chi-restraints excluded: chain D residue 1503 ASP Chi-restraints excluded: chain D residue 1526 ILE Chi-restraints excluded: chain D residue 1545 LEU Chi-restraints excluded: chain D residue 1546 GLU Chi-restraints excluded: chain D residue 1640 LEU Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1734 VAL Chi-restraints excluded: chain D residue 2183 TYR Chi-restraints excluded: chain D residue 2194 MET Chi-restraints excluded: chain D residue 2224 ASP Chi-restraints excluded: chain D residue 2231 LEU Chi-restraints excluded: chain D residue 2254 MET Chi-restraints excluded: chain D residue 2256 VAL Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2409 LEU Chi-restraints excluded: chain D residue 2410 ASP Chi-restraints excluded: chain D residue 2475 ILE Chi-restraints excluded: chain D residue 2513 ASP Chi-restraints excluded: chain D residue 2607 VAL Chi-restraints excluded: chain D residue 2748 THR Chi-restraints excluded: chain D residue 2833 LEU Chi-restraints excluded: chain D residue 2859 ILE Chi-restraints excluded: chain D residue 2894 VAL Chi-restraints excluded: chain D residue 2946 VAL Chi-restraints excluded: chain D residue 3012 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 712 VAL Chi-restraints excluded: chain E residue 738 PHE Chi-restraints excluded: chain E residue 745 THR Chi-restraints excluded: chain E residue 777 ASP Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 893 SER Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 916 ILE Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 1047 VAL Chi-restraints excluded: chain E residue 1147 LEU Chi-restraints excluded: chain E residue 1158 ASP Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1243 ILE Chi-restraints excluded: chain E residue 1265 LEU Chi-restraints excluded: chain E residue 1331 MET Chi-restraints excluded: chain E residue 1356 MET Chi-restraints excluded: chain E residue 1406 HIS Chi-restraints excluded: chain E residue 1443 ILE Chi-restraints excluded: chain E residue 1445 CYS Chi-restraints excluded: chain E residue 1447 HIS Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1526 ILE Chi-restraints excluded: chain E residue 1545 LEU Chi-restraints excluded: chain E residue 1567 LEU Chi-restraints excluded: chain E residue 1640 LEU Chi-restraints excluded: chain E residue 2194 MET Chi-restraints excluded: chain E residue 2224 ASP Chi-restraints excluded: chain E residue 2231 LEU Chi-restraints excluded: chain E residue 2258 LEU Chi-restraints excluded: chain E residue 2410 ASP Chi-restraints excluded: chain E residue 2421 GLN Chi-restraints excluded: chain E residue 2513 ASP Chi-restraints excluded: chain E residue 2544 VAL Chi-restraints excluded: chain E residue 2607 VAL Chi-restraints excluded: chain E residue 2740 ILE Chi-restraints excluded: chain E residue 2748 THR Chi-restraints excluded: chain E residue 2762 LEU Chi-restraints excluded: chain E residue 2859 ILE Chi-restraints excluded: chain E residue 2884 LYS Chi-restraints excluded: chain E residue 2946 VAL Chi-restraints excluded: chain E residue 3012 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 712 VAL Chi-restraints excluded: chain F residue 738 PHE Chi-restraints excluded: chain F residue 777 ASP Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 799 PHE Chi-restraints excluded: chain F residue 849 LEU Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 1039 THR Chi-restraints excluded: chain F residue 1047 VAL Chi-restraints excluded: chain F residue 1097 LEU Chi-restraints excluded: chain F residue 1158 ASP Chi-restraints excluded: chain F residue 1160 ASP Chi-restraints excluded: chain F residue 1181 THR Chi-restraints excluded: chain F residue 1189 LEU Chi-restraints excluded: chain F residue 1243 ILE Chi-restraints excluded: chain F residue 1265 LEU Chi-restraints excluded: chain F residue 1266 SER Chi-restraints excluded: chain F residue 1307 VAL Chi-restraints excluded: chain F residue 1319 VAL Chi-restraints excluded: chain F residue 1331 MET Chi-restraints excluded: chain F residue 1395 THR Chi-restraints excluded: chain F residue 1471 VAL Chi-restraints excluded: chain F residue 1508 ASP Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1567 LEU Chi-restraints excluded: chain F residue 1695 VAL Chi-restraints excluded: chain F residue 1699 VAL Chi-restraints excluded: chain F residue 1713 LEU Chi-restraints excluded: chain F residue 2037 LEU Chi-restraints excluded: chain F residue 2038 VAL Chi-restraints excluded: chain F residue 2183 TYR Chi-restraints excluded: chain F residue 2224 ASP Chi-restraints excluded: chain F residue 2254 MET Chi-restraints excluded: chain F residue 2409 LEU Chi-restraints excluded: chain F residue 2513 ASP Chi-restraints excluded: chain F residue 2544 VAL Chi-restraints excluded: chain F residue 2666 LEU Chi-restraints excluded: chain F residue 2748 THR Chi-restraints excluded: chain F residue 2762 LEU Chi-restraints excluded: chain F residue 2859 ILE Chi-restraints excluded: chain F residue 2894 VAL Chi-restraints excluded: chain F residue 2946 VAL Chi-restraints excluded: chain F residue 3012 VAL Chi-restraints excluded: chain F residue 3051 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1662 random chunks: chunk 1047 optimal weight: 1.9990 chunk 1404 optimal weight: 10.0000 chunk 403 optimal weight: 10.0000 chunk 1215 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 366 optimal weight: 10.0000 chunk 1320 optimal weight: 0.1980 chunk 552 optimal weight: 0.9990 chunk 1356 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 243 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS C1405 HIS ** C2593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3033 GLN ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3033 GLN ** E1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1388 HIS E1403 HIS ** F2421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.110022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.075948 restraints weight = 291577.764| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.29 r_work: 0.3037 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 127536 Z= 0.167 Angle : 0.611 14.788 173910 Z= 0.300 Chirality : 0.043 0.284 20016 Planarity : 0.004 0.076 22932 Dihedral : 4.758 43.750 18080 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.55 % Allowed : 13.52 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.04 % 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: -0.50 (0.07), residues: 16572 helix: 1.25 (0.06), residues: 7446 sheet: -1.28 (0.11), residues: 2184 loop : -1.79 (0.07), residues: 6942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E2326 HIS 0.010 0.001 HIS E1403 PHE 0.030 0.001 PHE F1512 TYR 0.016 0.001 TYR A2183 ARG 0.016 0.000 ARG C1556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33696.40 seconds wall clock time: 583 minutes 35.24 seconds (35015.24 seconds total)