Starting phenix.real_space_refine on Mon Oct 13 12:43:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yz0_6862/10_2025/5yz0_6862.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yz0_6862/10_2025/5yz0_6862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5yz0_6862/10_2025/5yz0_6862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yz0_6862/10_2025/5yz0_6862.map" model { file = "/net/cci-nas-00/data/ceres_data/5yz0_6862/10_2025/5yz0_6862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yz0_6862/10_2025/5yz0_6862.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 20633 2.51 5 N 6250 2.21 5 O 6364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33371 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2362, 15007 Classifications: {'peptide': 2362} Incomplete info: {'truncation_to_alanine': 1186} Link IDs: {'CIS': 12, 'PTRANS': 87, 'TRANS': 2262} Chain breaks: 8 Unresolved chain link angles: 48 Unresolved non-hydrogen bonds: 4131 Unresolved non-hydrogen angles: 5248 Unresolved non-hydrogen dihedrals: 3450 Unresolved non-hydrogen chiralities: 404 Planarities with less than four sites: {'GLU:plan': 83, 'HIS:plan': 38, 'ARG:plan': 55, 'TYR:plan': 36, 'ASN:plan1': 43, 'GLN:plan1': 56, 'PHE:plan': 60, 'ASP:plan': 64, 'TRP:plan': 12} Unresolved non-hydrogen planarities: 2062 Chain: "B" Number of atoms: 15007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2362, 15007 Classifications: {'peptide': 2362} Incomplete info: {'truncation_to_alanine': 1186} Link IDs: {'CIS': 12, 'PTRANS': 87, 'TRANS': 2262} Chain breaks: 8 Unresolved chain link angles: 48 Unresolved non-hydrogen bonds: 4131 Unresolved non-hydrogen angles: 5248 Unresolved non-hydrogen dihedrals: 3450 Unresolved non-hydrogen chiralities: 404 Planarities with less than four sites: {'GLU:plan': 83, 'HIS:plan': 38, 'ARG:plan': 55, 'TYR:plan': 36, 'ASN:plan1': 43, 'GLN:plan1': 56, 'PHE:plan': 60, 'ASP:plan': 64, 'TRP:plan': 12} Unresolved non-hydrogen planarities: 2062 Chain: "C" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 1785 Classifications: {'peptide': 362} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 311} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 328} Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 1048 Unresolved non-hydrogen angles: 1309 Unresolved non-hydrogen dihedrals: 876 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'ARG:plan': 19, 'GLU:plan': 30, 'HIS:plan': 10, 'PHE:plan': 12, 'ASP:plan': 17, 'GLN:plan1': 20, 'ASN:plan1': 10, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 522 Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 1572 Classifications: {'peptide': 318} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 277} Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 288} Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 960 Unresolved non-hydrogen angles: 1198 Unresolved non-hydrogen dihedrals: 802 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'ARG:plan': 18, 'GLU:plan': 29, 'HIS:plan': 9, 'PHE:plan': 11, 'ASP:plan': 17, 'GLN:plan1': 19, 'ASN:plan1': 10, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 498 Time building chain proxies: 8.14, per 1000 atoms: 0.24 Number of scatterers: 33371 At special positions: 0 Unit cell: (145.6, 208, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 6364 8.00 N 6250 7.00 C 20633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A2226 " - pdb=" SG CYS A2326 " distance=2.04 Simple disulfide: pdb=" SG CYS B2226 " - pdb=" SG CYS B2326 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.4 microseconds 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10326 Finding SS restraints... Secondary structure from input PDB file: 297 helices and 4 sheets defined 70.9% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 18 Processing helix chain 'A' and resid 26 through 44 Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 50 through 71 removed outlier: 3.693A pdb=" N LYS A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Proline residue: A 63 - end of helix Processing helix chain 'A' and resid 77 through 91 removed outlier: 4.203A pdb=" N HIS A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 96 through 120 removed outlier: 3.645A pdb=" N ILE A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.789A pdb=" N LEU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 142 Proline residue: A 139 - end of helix Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 155 through 166 removed outlier: 4.021A pdb=" N HIS A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.884A pdb=" N MET A 175 " --> pdb=" O TRP A 171 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 removed outlier: 4.088A pdb=" N MET A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.508A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 262 through 280 Processing helix chain 'A' and resid 284 through 303 removed outlier: 3.580A pdb=" N LYS A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 337 through 356 removed outlier: 3.602A pdb=" N LEU A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 382 removed outlier: 3.608A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 380 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.526A pdb=" N MET A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 442 Proline residue: A 429 - end of helix removed outlier: 3.614A pdb=" N LEU A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 447 through 459 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 483 through 500 removed outlier: 3.583A pdb=" N VAL A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 516 removed outlier: 3.930A pdb=" N CYS A 507 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 537 removed outlier: 3.812A pdb=" N LYS A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Proline residue: A 528 - end of helix removed outlier: 3.806A pdb=" N THR A 533 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 559 Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.729A pdb=" N MET A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 596 removed outlier: 3.548A pdb=" N HIS A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 613 removed outlier: 3.795A pdb=" N CYS A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 Proline residue: A 630 - end of helix Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 641 through 653 removed outlier: 3.897A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TRP A 651 " --> pdb=" O ILE A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 663 Processing helix chain 'A' and resid 664 through 678 Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.810A pdb=" N VAL A 688 " --> pdb=" O SER A 684 " (cutoff:3.500A) Proline residue: A 689 - end of helix Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 702 through 716 Processing helix chain 'A' and resid 716 through 721 removed outlier: 4.021A pdb=" N GLY A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 716 through 721' Processing helix chain 'A' and resid 723 through 739 removed outlier: 4.191A pdb=" N THR A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) Proline residue: A 731 - end of helix Processing helix chain 'A' and resid 748 through 762 removed outlier: 3.600A pdb=" N GLU A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 761 " --> pdb=" O GLN A 757 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.583A pdb=" N ALA A 781 " --> pdb=" O PRO A 777 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 782 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 808 Processing helix chain 'A' and resid 813 through 826 removed outlier: 3.686A pdb=" N ARG A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 839 Processing helix chain 'A' and resid 841 through 848 removed outlier: 4.103A pdb=" N LEU A 845 " --> pdb=" O PHE A 841 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 866 removed outlier: 3.969A pdb=" N LYS A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 885 removed outlier: 3.822A pdb=" N VAL A 885 " --> pdb=" O LYS A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 904 removed outlier: 4.153A pdb=" N VAL A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 929 Processing helix chain 'A' and resid 934 through 946 removed outlier: 4.265A pdb=" N VAL A 938 " --> pdb=" O CYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 969 removed outlier: 3.767A pdb=" N ARG A 968 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 969 " --> pdb=" O ALA A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 991 removed outlier: 3.593A pdb=" N ALA A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 997 through 1012 Proline residue: A1008 - end of helix Processing helix chain 'A' and resid 1014 through 1030 removed outlier: 3.992A pdb=" N GLN A1020 " --> pdb=" O THR A1016 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A1023 " --> pdb=" O LYS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1049 removed outlier: 4.172A pdb=" N LEU A1040 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1068 Processing helix chain 'A' and resid 1103 through 1118 Proline residue: A1110 - end of helix Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1122 through 1137 removed outlier: 3.639A pdb=" N GLY A1129 " --> pdb=" O PRO A1125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A1133 " --> pdb=" O GLY A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'A' and resid 1152 through 1163 removed outlier: 3.788A pdb=" N MET A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1182 removed outlier: 3.562A pdb=" N THR A1177 " --> pdb=" O LYS A1173 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A1178 " --> pdb=" O MET A1174 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A1179 " --> pdb=" O MET A1175 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY A1181 " --> pdb=" O THR A1177 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A1182 " --> pdb=" O LEU A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1398 Processing helix chain 'A' and resid 1400 through 1414 removed outlier: 4.651A pdb=" N ALA A1408 " --> pdb=" O TYR A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1434 Processing helix chain 'A' and resid 1438 through 1444 removed outlier: 3.805A pdb=" N LEU A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1455 Processing helix chain 'A' and resid 1474 through 1482 Processing helix chain 'A' and resid 1486 through 1499 Processing helix chain 'A' and resid 1503 through 1520 removed outlier: 4.101A pdb=" N SER A1515 " --> pdb=" O PHE A1511 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A1516 " --> pdb=" O THR A1512 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A1518 " --> pdb=" O CYS A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1539 removed outlier: 4.131A pdb=" N THR A1525 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A1526 " --> pdb=" O PHE A1522 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A1527 " --> pdb=" O LYS A1523 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU A1528 " --> pdb=" O VAL A1524 " (cutoff:3.500A) Proline residue: A1530 - end of helix removed outlier: 3.647A pdb=" N LEU A1533 " --> pdb=" O LEU A1529 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A1539 " --> pdb=" O TYR A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1542 through 1559 removed outlier: 3.563A pdb=" N LEU A1556 " --> pdb=" O ILE A1552 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS A1557 " --> pdb=" O MET A1553 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS A1558 " --> pdb=" O ALA A1554 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A1559 " --> pdb=" O VAL A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1603 removed outlier: 3.766A pdb=" N VAL A1581 " --> pdb=" O SER A1577 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A1587 " --> pdb=" O SER A1583 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1603 " --> pdb=" O LEU A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1636 removed outlier: 3.732A pdb=" N ILE A1636 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1648 removed outlier: 4.012A pdb=" N ALA A1644 " --> pdb=" O THR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1664 removed outlier: 3.806A pdb=" N VAL A1655 " --> pdb=" O TYR A1651 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A1659 " --> pdb=" O VAL A1655 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER A1660 " --> pdb=" O MET A1656 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A1661 " --> pdb=" O HIS A1657 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A1664 " --> pdb=" O SER A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1682 removed outlier: 5.315A pdb=" N GLY A1674 " --> pdb=" O GLN A1670 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE A1675 " --> pdb=" O GLU A1671 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A1676 " --> pdb=" O HIS A1672 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A1677 " --> pdb=" O LEU A1673 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS A1678 " --> pdb=" O GLY A1674 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A1679 " --> pdb=" O PHE A1675 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A1680 " --> pdb=" O LEU A1676 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A1682 " --> pdb=" O LYS A1678 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1694 removed outlier: 4.304A pdb=" N VAL A1689 " --> pdb=" O GLU A1685 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A1690 " --> pdb=" O PRO A1686 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY A1691 " --> pdb=" O ASP A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1713 removed outlier: 3.864A pdb=" N GLN A1705 " --> pdb=" O SER A1701 " (cutoff:3.500A) Processing helix chain 'A' and resid 1717 through 1727 removed outlier: 4.114A pdb=" N CYS A1721 " --> pdb=" O ASP A1717 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A1724 " --> pdb=" O ALA A1720 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A1725 " --> pdb=" O CYS A1721 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1746 removed outlier: 3.702A pdb=" N LYS A1741 " --> pdb=" O HIS A1737 " (cutoff:3.500A) Processing helix chain 'A' and resid 1748 through 1763 removed outlier: 3.917A pdb=" N THR A1754 " --> pdb=" O SER A1750 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN A1757 " --> pdb=" O ILE A1753 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A1758 " --> pdb=" O THR A1754 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL A1759 " --> pdb=" O GLN A1755 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS A1760 " --> pdb=" O VAL A1756 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A1761 " --> pdb=" O ASN A1757 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A1762 " --> pdb=" O GLY A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1771 removed outlier: 3.537A pdb=" N LEU A1770 " --> pdb=" O THR A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1784 through 1791 Processing helix chain 'A' and resid 1799 through 1813 removed outlier: 4.206A pdb=" N LEU A1807 " --> pdb=" O ARG A1803 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A1808 " --> pdb=" O LEU A1804 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU A1809 " --> pdb=" O GLY A1805 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A1810 " --> pdb=" O GLN A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1835 removed outlier: 4.003A pdb=" N TYR A1820 " --> pdb=" O ILE A1816 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A1823 " --> pdb=" O PHE A1819 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A1828 " --> pdb=" O LYS A1824 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A1831 " --> pdb=" O ARG A1827 " (cutoff:3.500A) Proline residue: A1833 - end of helix Processing helix chain 'A' and resid 1842 through 1846 removed outlier: 3.793A pdb=" N GLN A1845 " --> pdb=" O GLY A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1869 removed outlier: 3.936A pdb=" N LEU A1857 " --> pdb=" O ARG A1853 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS A1858 " --> pdb=" O LEU A1854 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU A1859 " --> pdb=" O HIS A1855 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A1860 " --> pdb=" O MET A1856 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A1863 " --> pdb=" O GLU A1859 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS A1865 " --> pdb=" O GLU A1861 " (cutoff:3.500A) Proline residue: A1866 - end of helix removed outlier: 3.515A pdb=" N GLN A1869 " --> pdb=" O LYS A1865 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 3.607A pdb=" N ARG A1895 " --> pdb=" O ASN A1892 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS A1897 " --> pdb=" O TYR A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1904 through 1913 Processing helix chain 'A' and resid 1914 through 1916 No H-bonds generated for 'chain 'A' and resid 1914 through 1916' Processing helix chain 'A' and resid 1922 through 1937 removed outlier: 4.432A pdb=" N GLN A1926 " --> pdb=" O GLU A1922 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A1928 " --> pdb=" O TRP A1924 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS A1937 " --> pdb=" O LYS A1933 " (cutoff:3.500A) Processing helix chain 'A' and resid 1945 through 1951 removed outlier: 3.960A pdb=" N GLU A1949 " --> pdb=" O LEU A1945 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A1950 " --> pdb=" O ASN A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1958 through 1973 removed outlier: 3.878A pdb=" N SER A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A1966 " --> pdb=" O TRP A1962 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A1967 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP A1968 " --> pdb=" O TRP A1964 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A1969 " --> pdb=" O SER A1965 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS A1970 " --> pdb=" O LYS A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1983 removed outlier: 4.352A pdb=" N GLY A1979 " --> pdb=" O VAL A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 1989 Processing helix chain 'A' and resid 1997 through 2002 Processing helix chain 'A' and resid 2005 through 2010 Processing helix chain 'A' and resid 2012 through 2017 removed outlier: 4.016A pdb=" N PHE A2016 " --> pdb=" O GLU A2012 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A2017 " --> pdb=" O THR A2013 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2012 through 2017' Processing helix chain 'A' and resid 2021 through 2032 removed outlier: 3.538A pdb=" N TYR A2025 " --> pdb=" O ILE A2021 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A2030 " --> pdb=" O LYS A2026 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A2032 " --> pdb=" O VAL A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2032 through 2037 Processing helix chain 'A' and resid 2043 through 2057 removed outlier: 4.093A pdb=" N LYS A2048 " --> pdb=" O LYS A2044 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A2049 " --> pdb=" O TYR A2045 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET A2050 " --> pdb=" O TYR A2046 " (cutoff:3.500A) Proline residue: A2051 - end of helix removed outlier: 3.719A pdb=" N ASP A2055 " --> pdb=" O PRO A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2063 through 2078 removed outlier: 4.432A pdb=" N TYR A2067 " --> pdb=" O ASP A2063 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A2071 " --> pdb=" O TYR A2067 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE A2072 " --> pdb=" O ILE A2068 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A2076 " --> pdb=" O PHE A2072 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A2077 " --> pdb=" O GLY A2073 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A2078 " --> pdb=" O ARG A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2086 through 2109 removed outlier: 3.928A pdb=" N MET A2090 " --> pdb=" O SER A2086 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA A2101 " --> pdb=" O TYR A2097 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A2102 " --> pdb=" O GLY A2098 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A2103 " --> pdb=" O THR A2099 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A2108 " --> pdb=" O TRP A2104 " (cutoff:3.500A) Processing helix chain 'A' and resid 2111 through 2133 removed outlier: 4.176A pdb=" N ASN A2117 " --> pdb=" O VAL A2113 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A2127 " --> pdb=" O ASN A2123 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A2128 " --> pdb=" O LYS A2124 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS A2129 " --> pdb=" O VAL A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 4.243A pdb=" N PHE A2138 " --> pdb=" O ALA A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2141 through 2148 removed outlier: 3.906A pdb=" N ARG A2148 " --> pdb=" O GLN A2144 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2170 removed outlier: 3.678A pdb=" N LYS A2166 " --> pdb=" O GLU A2162 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA A2170 " --> pdb=" O LYS A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2173 through 2184 removed outlier: 4.294A pdb=" N TRP A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET A2178 " --> pdb=" O GLN A2174 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A2179 " --> pdb=" O ALA A2175 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR A2180 " --> pdb=" O MET A2176 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A2181 " --> pdb=" O TRP A2177 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL A2182 " --> pdb=" O MET A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2187 through 2203 removed outlier: 3.822A pdb=" N GLU A2196 " --> pdb=" O ASN A2192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A2201 " --> pdb=" O ILE A2197 " (cutoff:3.500A) Processing helix chain 'A' and resid 2204 through 2207 removed outlier: 7.183A pdb=" N SER A2207 " --> pdb=" O MET A2204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2204 through 2207' Processing helix chain 'A' and resid 2208 through 2228 removed outlier: 3.730A pdb=" N THR A2216 " --> pdb=" O VAL A2212 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A2221 " --> pdb=" O ARG A2217 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A2224 " --> pdb=" O ASP A2220 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS A2226 " --> pdb=" O LEU A2222 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2249 Processing helix chain 'A' and resid 2249 through 2254 Processing helix chain 'A' and resid 2332 through 2352 removed outlier: 3.805A pdb=" N ARG A2337 " --> pdb=" O ARG A2333 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A2338 " --> pdb=" O LYS A2334 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A2343 " --> pdb=" O MET A2339 " (cutoff:3.500A) Processing helix chain 'A' and resid 2353 through 2359 Processing helix chain 'A' and resid 2385 through 2397 removed outlier: 4.403A pdb=" N LEU A2393 " --> pdb=" O ILE A2389 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR A2394 " --> pdb=" O LEU A2390 " (cutoff:3.500A) Processing helix chain 'A' and resid 2416 through 2429 removed outlier: 3.999A pdb=" N LEU A2429 " --> pdb=" O ARG A2425 " (cutoff:3.500A) Processing helix chain 'A' and resid 2434 through 2443 Processing helix chain 'A' and resid 2448 through 2471 removed outlier: 3.517A pdb=" N SER A2453 " --> pdb=" O SER A2449 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A2459 " --> pdb=" O SER A2455 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A2463 " --> pdb=" O ARG A2459 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET A2464 " --> pdb=" O SER A2460 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2505 Processing helix chain 'A' and resid 2516 through 2523 removed outlier: 4.364A pdb=" N MET A2523 " --> pdb=" O MET A2519 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2546 removed outlier: 3.939A pdb=" N ARG A2534 " --> pdb=" O GLY A2530 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A2538 " --> pdb=" O ARG A2534 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A2539 " --> pdb=" O ALA A2535 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A2540 " --> pdb=" O CYS A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2547 through 2552 removed outlier: 3.907A pdb=" N SER A2552 " --> pdb=" O GLU A2548 " (cutoff:3.500A) Processing helix chain 'A' and resid 2552 through 2559 Processing helix chain 'A' and resid 2587 through 2597 removed outlier: 3.651A pdb=" N LEU A2593 " --> pdb=" O LYS A2589 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A2596 " --> pdb=" O VAL A2592 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2626 removed outlier: 4.325A pdb=" N HIS A2621 " --> pdb=" O GLU A2617 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A2622 " --> pdb=" O GLY A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2629 through 2634 Processing helix chain 'A' and resid 2635 through 2636 No H-bonds generated for 'chain 'A' and resid 2635 through 2636' Processing helix chain 'A' and resid 2637 through 2641 Processing helix chain 'B' and resid 3 through 17 removed outlier: 4.230A pdb=" N SER B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 11 " --> pdb=" O GLU B 7 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 12 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Proline residue: B 13 - end of helix Processing helix chain 'B' and resid 26 through 44 Proline residue: B 33 - end of helix removed outlier: 3.869A pdb=" N ILE B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 44 " --> pdb=" O PHE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 71 removed outlier: 3.641A pdb=" N ASP B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.531A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 120 removed outlier: 3.598A pdb=" N THR B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix removed outlier: 4.422A pdb=" N LEU B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 144 removed outlier: 3.537A pdb=" N ILE B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Proline residue: B 139 - end of helix Processing helix chain 'B' and resid 146 through 153 removed outlier: 4.976A pdb=" N GLN B 151 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 170 through 188 removed outlier: 3.892A pdb=" N MET B 175 " --> pdb=" O TRP B 171 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 179 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 212 through 219 removed outlier: 3.574A pdb=" N ILE B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'B' and resid 235 through 250 Proline residue: B 242 - end of helix Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 262 through 279 removed outlier: 3.700A pdb=" N THR B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 277 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 303 Proline residue: B 294 - end of helix Processing helix chain 'B' and resid 312 through 328 Processing helix chain 'B' and resid 337 through 355 removed outlier: 4.281A pdb=" N GLN B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 383 removed outlier: 3.610A pdb=" N CYS B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 396 removed outlier: 3.513A pdb=" N LEU B 396 " --> pdb=" O LEU B 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 393 through 396' Processing helix chain 'B' and resid 397 through 416 removed outlier: 3.875A pdb=" N MET B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 442 Proline residue: B 429 - end of helix Proline residue: B 440 - end of helix Processing helix chain 'B' and resid 446 through 459 removed outlier: 3.569A pdb=" N GLU B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 removed outlier: 3.654A pdb=" N ILE B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 478 " --> pdb=" O GLN B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 483 through 500 removed outlier: 3.623A pdb=" N THR B 500 " --> pdb=" O VAL B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 516 Processing helix chain 'B' and resid 521 through 536 removed outlier: 3.561A pdb=" N LYS B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) Proline residue: B 528 - end of helix removed outlier: 3.951A pdb=" N THR B 533 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TRP B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 558 removed outlier: 3.675A pdb=" N SER B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 572 removed outlier: 3.865A pdb=" N VAL B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 596 removed outlier: 3.505A pdb=" N ASP B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 596 " --> pdb=" O GLY B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 613 removed outlier: 3.715A pdb=" N HIS B 602 " --> pdb=" O TRP B 598 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 611 " --> pdb=" O CYS B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 635 Proline residue: B 630 - end of helix Processing helix chain 'B' and resid 641 through 653 removed outlier: 4.704A pdb=" N ARG B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE B 647 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP B 651 " --> pdb=" O ILE B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 678 removed outlier: 3.535A pdb=" N SER B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 696 removed outlier: 3.863A pdb=" N CYS B 685 " --> pdb=" O GLN B 681 " (cutoff:3.500A) Proline residue: B 689 - end of helix Processing helix chain 'B' and resid 700 through 720 Processing helix chain 'B' and resid 723 through 739 removed outlier: 3.922A pdb=" N THR B 729 " --> pdb=" O THR B 725 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Proline residue: B 731 - end of helix Processing helix chain 'B' and resid 749 through 764 Processing helix chain 'B' and resid 775 through 788 removed outlier: 3.695A pdb=" N ASP B 784 " --> pdb=" O LEU B 780 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 785 " --> pdb=" O ALA B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.683A pdb=" N ARG B 796 " --> pdb=" O HIS B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 808 removed outlier: 3.682A pdb=" N LYS B 803 " --> pdb=" O GLU B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 826 removed outlier: 4.470A pdb=" N ALA B 823 " --> pdb=" O ASP B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 839 Processing helix chain 'B' and resid 841 through 846 Processing helix chain 'B' and resid 849 through 866 removed outlier: 4.402A pdb=" N ALA B 853 " --> pdb=" O ARG B 849 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR B 854 " --> pdb=" O MET B 850 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR B 855 " --> pdb=" O LYS B 851 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B 856 " --> pdb=" O GLU B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 885 Processing helix chain 'B' and resid 889 through 901 removed outlier: 3.618A pdb=" N CYS B 895 " --> pdb=" O HIS B 891 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 897 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 898 " --> pdb=" O HIS B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 931 removed outlier: 3.559A pdb=" N LYS B 930 " --> pdb=" O PHE B 926 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 931 " --> pdb=" O SER B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 949 removed outlier: 3.728A pdb=" N VAL B 938 " --> pdb=" O CYS B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 968 removed outlier: 3.573A pdb=" N LYS B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 991 Proline residue: B 985 - end of helix Processing helix chain 'B' and resid 999 through 1011 removed outlier: 3.845A pdb=" N ALA B1003 " --> pdb=" O LEU B 999 " (cutoff:3.500A) Proline residue: B1008 - end of helix removed outlier: 3.958A pdb=" N SER B1011 " --> pdb=" O SER B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1031 removed outlier: 3.561A pdb=" N LEU B1029 " --> pdb=" O ARG B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 removed outlier: 4.274A pdb=" N SER B1043 " --> pdb=" O LEU B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1066 Processing helix chain 'B' and resid 1103 through 1115 Proline residue: B1110 - end of helix Processing helix chain 'B' and resid 1122 through 1136 removed outlier: 3.783A pdb=" N PHE B1133 " --> pdb=" O GLY B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1163 Processing helix chain 'B' and resid 1168 through 1175 removed outlier: 4.075A pdb=" N LYS B1173 " --> pdb=" O SER B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1175 through 1180 removed outlier: 3.642A pdb=" N ARG B1179 " --> pdb=" O MET B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1384 through 1398 removed outlier: 3.837A pdb=" N GLU B1388 " --> pdb=" O VAL B1384 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B1392 " --> pdb=" O GLU B1388 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B1393 " --> pdb=" O ASP B1389 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B1397 " --> pdb=" O ALA B1393 " (cutoff:3.500A) Processing helix chain 'B' and resid 1401 through 1414 removed outlier: 3.977A pdb=" N ALA B1408 " --> pdb=" O TYR B1404 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1417 No H-bonds generated for 'chain 'B' and resid 1415 through 1417' Processing helix chain 'B' and resid 1420 through 1433 removed outlier: 4.652A pdb=" N ILE B1427 " --> pdb=" O GLU B1423 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR B1428 " --> pdb=" O LEU B1424 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1443 Processing helix chain 'B' and resid 1446 through 1455 Processing helix chain 'B' and resid 1471 through 1479 Proline residue: B1477 - end of helix Processing helix chain 'B' and resid 1486 through 1499 Processing helix chain 'B' and resid 1503 through 1520 removed outlier: 3.765A pdb=" N ALA B1507 " --> pdb=" O ARG B1503 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B1508 " --> pdb=" O HIS B1504 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS B1509 " --> pdb=" O ASP B1505 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS B1519 " --> pdb=" O SER B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1521 through 1527 removed outlier: 3.590A pdb=" N ILE B1526 " --> pdb=" O PHE B1522 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B1527 " --> pdb=" O LYS B1523 " (cutoff:3.500A) Processing helix chain 'B' and resid 1528 through 1537 Processing helix chain 'B' and resid 1541 through 1543 No H-bonds generated for 'chain 'B' and resid 1541 through 1543' Processing helix chain 'B' and resid 1544 through 1558 removed outlier: 3.576A pdb=" N ILE B1552 " --> pdb=" O VAL B1548 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B1554 " --> pdb=" O ALA B1550 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B1556 " --> pdb=" O ILE B1552 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS B1558 " --> pdb=" O ALA B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1573 through 1601 removed outlier: 3.501A pdb=" N GLN B1579 " --> pdb=" O GLN B1575 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B1580 " --> pdb=" O LEU B1576 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B1581 " --> pdb=" O SER B1577 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B1585 " --> pdb=" O VAL B1581 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B1590 " --> pdb=" O ASP B1586 " (cutoff:3.500A) Processing helix chain 'B' and resid 1616 through 1634 Processing helix chain 'B' and resid 1638 through 1648 removed outlier: 3.515A pdb=" N ALA B1644 " --> pdb=" O THR B1640 " (cutoff:3.500A) Processing helix chain 'B' and resid 1652 through 1664 removed outlier: 3.582A pdb=" N GLU B1659 " --> pdb=" O VAL B1655 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B1660 " --> pdb=" O MET B1656 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B1663 " --> pdb=" O GLU B1659 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B1664 " --> pdb=" O SER B1660 " (cutoff:3.500A) Processing helix chain 'B' and resid 1674 through 1683 removed outlier: 4.198A pdb=" N LYS B1678 " --> pdb=" O GLY B1674 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B1679 " --> pdb=" O PHE B1675 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET B1683 " --> pdb=" O LEU B1679 " (cutoff:3.500A) Processing helix chain 'B' and resid 1685 through 1694 removed outlier: 3.806A pdb=" N VAL B1689 " --> pdb=" O GLU B1685 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B1690 " --> pdb=" O PRO B1686 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B1693 " --> pdb=" O VAL B1689 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B1694 " --> pdb=" O ALA B1690 " (cutoff:3.500A) Processing helix chain 'B' and resid 1701 through 1708 Processing helix chain 'B' and resid 1708 through 1713 removed outlier: 3.835A pdb=" N GLY B1713 " --> pdb=" O HIS B1709 " (cutoff:3.500A) Processing helix chain 'B' and resid 1717 through 1729 Processing helix chain 'B' and resid 1733 through 1746 removed outlier: 3.585A pdb=" N VAL B1740 " --> pdb=" O TYR B1736 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B1741 " --> pdb=" O HIS B1737 " (cutoff:3.500A) Processing helix chain 'B' and resid 1748 through 1761 removed outlier: 4.595A pdb=" N ASN B1757 " --> pdb=" O ILE B1753 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY B1758 " --> pdb=" O THR B1754 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL B1759 " --> pdb=" O GLN B1755 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N HIS B1760 " --> pdb=" O VAL B1756 " (cutoff:3.500A) Processing helix chain 'B' and resid 1769 through 1774 Processing helix chain 'B' and resid 1776 through 1780 Processing helix chain 'B' and resid 1784 through 1791 removed outlier: 3.537A pdb=" N LEU B1791 " --> pdb=" O VAL B1787 " (cutoff:3.500A) Processing helix chain 'B' and resid 1801 through 1813 removed outlier: 3.982A pdb=" N LEU B1808 " --> pdb=" O LEU B1804 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B1809 " --> pdb=" O GLY B1805 " (cutoff:3.500A) Processing helix chain 'B' and resid 1815 through 1827 removed outlier: 3.640A pdb=" N VAL B1826 " --> pdb=" O SER B1822 " (cutoff:3.500A) Processing helix chain 'B' and resid 1842 through 1847 removed outlier: 4.240A pdb=" N GLY B1847 " --> pdb=" O SER B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1847 through 1865 removed outlier: 4.168A pdb=" N LEU B1857 " --> pdb=" O ARG B1853 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N CYS B1858 " --> pdb=" O LEU B1854 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B1859 " --> pdb=" O HIS B1855 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER B1863 " --> pdb=" O GLU B1859 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B1865 " --> pdb=" O GLU B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1866 through 1868 No H-bonds generated for 'chain 'B' and resid 1866 through 1868' Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 3.721A pdb=" N ARG B1895 " --> pdb=" O ASN B1892 " (cutoff:3.500A) Processing helix chain 'B' and resid 1904 through 1913 removed outlier: 4.620A pdb=" N LEU B1910 " --> pdb=" O ALA B1906 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B1913 " --> pdb=" O SER B1909 " (cutoff:3.500A) Processing helix chain 'B' and resid 1913 through 1918 Processing helix chain 'B' and resid 1922 through 1939 removed outlier: 3.873A pdb=" N GLN B1926 " --> pdb=" O GLU B1922 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B1928 " --> pdb=" O TRP B1924 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B1933 " --> pdb=" O ARG B1929 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY B1935 " --> pdb=" O ALA B1931 " (cutoff:3.500A) Processing helix chain 'B' and resid 1943 through 1945 No H-bonds generated for 'chain 'B' and resid 1943 through 1945' Processing helix chain 'B' and resid 1946 through 1951 removed outlier: 3.546A pdb=" N SER B1950 " --> pdb=" O ASN B1946 " (cutoff:3.500A) Processing helix chain 'B' and resid 1958 through 1973 removed outlier: 3.665A pdb=" N ASP B1968 " --> pdb=" O TRP B1964 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS B1970 " --> pdb=" O LYS B1966 " (cutoff:3.500A) Processing helix chain 'B' and resid 1975 through 1983 Processing helix chain 'B' and resid 1997 through 2005 removed outlier: 3.778A pdb=" N MET B2003 " --> pdb=" O HIS B1999 " (cutoff:3.500A) Processing helix chain 'B' and resid 2011 through 2016 removed outlier: 3.807A pdb=" N ALA B2014 " --> pdb=" O GLU B2011 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B2015 " --> pdb=" O GLU B2012 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2032 removed outlier: 3.979A pdb=" N TYR B2025 " --> pdb=" O ILE B2021 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B2030 " --> pdb=" O LYS B2026 " (cutoff:3.500A) Processing helix chain 'B' and resid 2042 through 2057 removed outlier: 3.915A pdb=" N TYR B2046 " --> pdb=" O LEU B2042 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET B2050 " --> pdb=" O TYR B2046 " (cutoff:3.500A) Proline residue: B2051 - end of helix removed outlier: 3.791A pdb=" N ASN B2056 " --> pdb=" O MET B2052 " (cutoff:3.500A) Processing helix chain 'B' and resid 2064 through 2078 removed outlier: 3.929A pdb=" N ILE B2068 " --> pdb=" O LEU B2064 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B2071 " --> pdb=" O TYR B2067 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B2072 " --> pdb=" O ILE B2068 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B2073 " --> pdb=" O VAL B2069 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG B2074 " --> pdb=" O LEU B2070 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B2076 " --> pdb=" O PHE B2072 " (cutoff:3.500A) Processing helix chain 'B' and resid 2086 through 2100 removed outlier: 3.527A pdb=" N MET B2090 " --> pdb=" O SER B2086 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B2099 " --> pdb=" O LEU B2095 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) Processing helix chain 'B' and resid 2101 through 2109 Processing helix chain 'B' and resid 2111 through 2133 removed outlier: 4.170A pdb=" N MET B2115 " --> pdb=" O ASP B2111 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN B2117 " --> pdb=" O VAL B2113 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B2125 " --> pdb=" O LYS B2121 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B2127 " --> pdb=" O ASN B2123 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B2128 " --> pdb=" O LYS B2124 " (cutoff:3.500A) Processing helix chain 'B' and resid 2134 through 2139 Processing helix chain 'B' and resid 2141 through 2148 Processing helix chain 'B' and resid 2153 through 2169 removed outlier: 3.533A pdb=" N ALA B2165 " --> pdb=" O MET B2161 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2184 removed outlier: 3.977A pdb=" N ALA B2175 " --> pdb=" O TYR B2171 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B2178 " --> pdb=" O GLN B2174 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B2180 " --> pdb=" O MET B2176 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA B2181 " --> pdb=" O TRP B2177 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL B2182 " --> pdb=" O MET B2178 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS B2184 " --> pdb=" O THR B2180 " (cutoff:3.500A) Processing helix chain 'B' and resid 2187 through 2203 removed outlier: 3.598A pdb=" N ARG B2193 " --> pdb=" O MET B2189 " (cutoff:3.500A) Processing helix chain 'B' and resid 2208 through 2228 removed outlier: 3.708A pdb=" N VAL B2212 " --> pdb=" O LEU B2208 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS B2226 " --> pdb=" O LEU B2222 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2249 Processing helix chain 'B' and resid 2249 through 2254 removed outlier: 3.783A pdb=" N ALA B2253 " --> pdb=" O LEU B2249 " (cutoff:3.500A) Processing helix chain 'B' and resid 2332 through 2352 removed outlier: 3.872A pdb=" N ARG B2337 " --> pdb=" O ARG B2333 " (cutoff:3.500A) Processing helix chain 'B' and resid 2352 through 2358 removed outlier: 4.278A pdb=" N ARG B2356 " --> pdb=" O ASP B2352 " (cutoff:3.500A) Processing helix chain 'B' and resid 2385 through 2395 Processing helix chain 'B' and resid 2416 through 2426 Processing helix chain 'B' and resid 2434 through 2443 removed outlier: 4.199A pdb=" N LEU B2441 " --> pdb=" O HIS B2437 " (cutoff:3.500A) Processing helix chain 'B' and resid 2450 through 2472 removed outlier: 4.179A pdb=" N ARG B2459 " --> pdb=" O SER B2455 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B2461 " --> pdb=" O TYR B2457 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B2463 " --> pdb=" O ARG B2459 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B2464 " --> pdb=" O SER B2460 " (cutoff:3.500A) Processing helix chain 'B' and resid 2516 through 2522 Processing helix chain 'B' and resid 2530 through 2546 removed outlier: 3.606A pdb=" N VAL B2538 " --> pdb=" O ARG B2534 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B2540 " --> pdb=" O CYS B2536 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B2546 " --> pdb=" O LEU B2542 " (cutoff:3.500A) Processing helix chain 'B' and resid 2546 through 2559 removed outlier: 3.655A pdb=" N LEU B2550 " --> pdb=" O GLN B2546 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B2552 " --> pdb=" O GLU B2548 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B2553 " --> pdb=" O PRO B2549 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B2554 " --> pdb=" O LEU B2550 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B2555 " --> pdb=" O MET B2551 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B2556 " --> pdb=" O SER B2552 " (cutoff:3.500A) Processing helix chain 'B' and resid 2587 through 2599 removed outlier: 3.664A pdb=" N GLU B2596 " --> pdb=" O VAL B2592 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B2598 " --> pdb=" O ASP B2594 " (cutoff:3.500A) Processing helix chain 'B' and resid 2615 through 2629 removed outlier: 3.848A pdb=" N LEU B2623 " --> pdb=" O HIS B2619 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B2625 " --> pdb=" O HIS B2621 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B2627 " --> pdb=" O LEU B2623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B2628 " --> pdb=" O ILE B2624 " (cutoff:3.500A) Processing helix chain 'B' and resid 2629 through 2635 removed outlier: 3.609A pdb=" N CYS B2634 " --> pdb=" O GLU B2630 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B2635 " --> pdb=" O ASN B2631 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 29 through 42 Processing helix chain 'C' and resid 42 through 50 removed outlier: 4.517A pdb=" N ASP C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Proline residue: C 48 - end of helix Processing helix chain 'C' and resid 65 through 74 removed outlier: 3.659A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 4.211A pdb=" N VAL C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N HIS C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG C 89 " --> pdb=" O HIS C 85 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 93 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.511A pdb=" N LEU C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS C 122 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.644A pdb=" N LEU C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 160 removed outlier: 3.589A pdb=" N LEU C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 159 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 176 through 180 removed outlier: 4.109A pdb=" N LYS C 179 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 208 through 213 removed outlier: 3.578A pdb=" N ASN C 213 " --> pdb=" O SER C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 231 Proline residue: C 225 - end of helix Proline residue: C 229 - end of helix Processing helix chain 'C' and resid 237 through 251 Proline residue: C 248 - end of helix removed outlier: 3.565A pdb=" N GLU C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.565A pdb=" N GLY C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 297 through 319 removed outlier: 3.574A pdb=" N ARG C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU C 317 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 346 Proline residue: C 340 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 350 through 361 Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.570A pdb=" N ARG D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 74 removed outlier: 3.599A pdb=" N GLN D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 87 removed outlier: 4.356A pdb=" N HIS D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 107 through 122 removed outlier: 3.712A pdb=" N LYS D 122 " --> pdb=" O GLN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 137 removed outlier: 3.595A pdb=" N VAL D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU D 132 " --> pdb=" O MET D 128 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU D 133 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 158 removed outlier: 3.530A pdb=" N SER D 154 " --> pdb=" O HIS D 150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.644A pdb=" N PHE D 194 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.638A pdb=" N ALA D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 228 Proline residue: D 225 - end of helix Processing helix chain 'D' and resid 238 through 255 Proline residue: D 248 - end of helix Processing helix chain 'D' and resid 268 through 279 removed outlier: 4.398A pdb=" N GLY D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 284 removed outlier: 4.253A pdb=" N LEU D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG D 284 " --> pdb=" O PRO D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 279 through 284' Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.632A pdb=" N ILE D 311 " --> pdb=" O THR D 307 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2243 through 2244 removed outlier: 7.348A pdb=" N MET A2299 " --> pdb=" O SER A2313 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER A2313 " --> pdb=" O MET A2299 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A2310 " --> pdb=" O CYS A2326 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS A2326 " --> pdb=" O LYS A2310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2481 through 2483 Processing sheet with id=AA3, first strand: chain 'B' and resid 2243 through 2244 removed outlier: 7.433A pdb=" N MET B2299 " --> pdb=" O SER B2313 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER B2313 " --> pdb=" O MET B2299 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS B2310 " --> pdb=" O CYS B2326 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS B2326 " --> pdb=" O LYS B2310 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE B2323 " --> pdb=" O TRP B2379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2481 through 2483 2089 hydrogen bonds defined for protein. 6177 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: 8.65 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11889 1.34 - 1.46: 7405 1.46 - 1.59: 14235 1.59 - 1.71: 0 1.71 - 1.84: 208 Bond restraints: 33737 Sorted by residual: bond pdb=" C THR A2641 " pdb=" O THR A2641 " ideal model delta sigma weight residual 1.235 1.261 -0.026 4.70e-03 4.53e+04 3.04e+01 bond pdb=" CB ASN B2080 " pdb=" CG ASN B2080 " ideal model delta sigma weight residual 1.516 1.435 0.081 2.50e-02 1.60e+03 1.05e+01 bond pdb=" C LYS B2308 " pdb=" N PRO B2309 " ideal model delta sigma weight residual 1.329 1.367 -0.038 1.20e-02 6.94e+03 9.99e+00 bond pdb=" CA ALA A2020 " pdb=" CB ALA A2020 " ideal model delta sigma weight residual 1.530 1.485 0.045 1.48e-02 4.57e+03 9.31e+00 bond pdb=" CB TRP B1779 " pdb=" CG TRP B1779 " ideal model delta sigma weight residual 1.498 1.410 0.088 3.10e-02 1.04e+03 8.03e+00 ... (remaining 33732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 44290 2.95 - 5.91: 1525 5.91 - 8.86: 408 8.86 - 11.81: 39 11.81 - 14.77: 14 Bond angle restraints: 46276 Sorted by residual: angle pdb=" N PRO D 24 " pdb=" CA PRO D 24 " pdb=" CB PRO D 24 " ideal model delta sigma weight residual 102.81 109.85 -7.04 6.70e-01 2.23e+00 1.10e+02 angle pdb=" N PRO D 235 " pdb=" CA PRO D 235 " pdb=" CB PRO D 235 " ideal model delta sigma weight residual 101.88 111.00 -9.12 1.01e+00 9.80e-01 8.16e+01 angle pdb=" N PRO A 358 " pdb=" CA PRO A 358 " pdb=" CB PRO A 358 " ideal model delta sigma weight residual 103.25 111.99 -8.74 1.05e+00 9.07e-01 6.93e+01 angle pdb=" N PRO A1189 " pdb=" CA PRO A1189 " pdb=" CB PRO A1189 " ideal model delta sigma weight residual 103.25 111.88 -8.63 1.05e+00 9.07e-01 6.75e+01 angle pdb=" N PRO D 107 " pdb=" CA PRO D 107 " pdb=" CB PRO D 107 " ideal model delta sigma weight residual 103.25 111.85 -8.60 1.05e+00 9.07e-01 6.70e+01 ... (remaining 46271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 18721 14.96 - 29.92: 1225 29.92 - 44.87: 156 44.87 - 59.83: 35 59.83 - 74.79: 7 Dihedral angle restraints: 20144 sinusoidal: 4350 harmonic: 15794 Sorted by residual: dihedral pdb=" CA GLU A2564 " pdb=" C GLU A2564 " pdb=" N TRP A2565 " pdb=" CA TRP A2565 " ideal model delta harmonic sigma weight residual -180.00 -107.52 -72.48 0 5.00e+00 4.00e-02 2.10e+02 dihedral pdb=" CA ARG A1846 " pdb=" C ARG A1846 " pdb=" N GLY A1847 " pdb=" CA GLY A1847 " ideal model delta harmonic sigma weight residual 180.00 111.61 68.39 0 5.00e+00 4.00e-02 1.87e+02 dihedral pdb=" CA ARG B1846 " pdb=" C ARG B1846 " pdb=" N GLY B1847 " pdb=" CA GLY B1847 " ideal model delta harmonic sigma weight residual 180.00 116.38 63.62 0 5.00e+00 4.00e-02 1.62e+02 ... (remaining 20141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4827 0.078 - 0.156: 700 0.156 - 0.234: 119 0.234 - 0.312: 97 0.312 - 0.390: 10 Chirality restraints: 5753 Sorted by residual: chirality pdb=" CA PRO B 445 " pdb=" N PRO B 445 " pdb=" C PRO B 445 " pdb=" CB PRO B 445 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA PRO A 445 " pdb=" N PRO A 445 " pdb=" C PRO A 445 " pdb=" CB PRO A 445 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CG LEU A2076 " pdb=" CB LEU A2076 " pdb=" CD1 LEU A2076 " pdb=" CD2 LEU A2076 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 5750 not shown) Planarity restraints: 6264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B1984 " -0.087 5.00e-02 4.00e+02 1.32e-01 2.81e+01 pdb=" N PRO B1985 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO B1985 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO B1985 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1984 " 0.086 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO A1985 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO A1985 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A1985 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1776 " -0.023 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C GLU B1776 " 0.082 2.00e-02 2.50e+03 pdb=" O GLU B1776 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA B1777 " -0.028 2.00e-02 2.50e+03 ... (remaining 6261 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1574 2.70 - 3.25: 37924 3.25 - 3.80: 56917 3.80 - 4.35: 70489 4.35 - 4.90: 96294 Nonbonded interactions: 263198 Sorted by model distance: nonbonded pdb=" O PHE B1184 " pdb=" OH TYR B1844 " model vdw 2.154 3.040 nonbonded pdb=" O PHE A1184 " pdb=" OH TYR A1844 " model vdw 2.195 3.040 nonbonded pdb=" O LYS B2587 " pdb=" OG1 THR B2590 " model vdw 2.214 3.040 nonbonded pdb=" O ALA B1642 " pdb=" OG SER B1645 " model vdw 2.222 3.040 nonbonded pdb=" O LYS A2587 " pdb=" OG1 THR A2590 " model vdw 2.224 3.040 ... (remaining 263193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 5 through 322) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.570 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 0.088 33739 Z= 0.421 Angle : 1.371 14.768 46280 Z= 0.860 Chirality : 0.069 0.390 5753 Planarity : 0.007 0.132 6264 Dihedral : 11.419 74.788 9812 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 1.68 % Allowed : 15.57 % Favored : 82.76 % Rotamer: Outliers : 0.97 % Allowed : 3.30 % Favored : 95.73 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.47 % Twisted Proline : 7.30 % Twisted General : 1.86 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.74 (0.09), residues: 5364 helix: -3.23 (0.06), residues: 2599 sheet: -3.15 (0.65), residues: 56 loop : -3.07 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A1774 TYR 0.050 0.004 TYR B1535 PHE 0.050 0.003 PHE A2436 TRP 0.032 0.004 TRP B2104 HIS 0.024 0.005 HIS B2492 Details of bonding type rmsd covalent geometry : bond 0.00794 (33737) covalent geometry : angle 1.37070 (46276) SS BOND : bond 0.00780 ( 2) SS BOND : angle 3.76564 ( 4) hydrogen bonds : bond 0.34207 ( 2089) hydrogen bonds : angle 9.53269 ( 6177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 640 time to evaluate : 1.259 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: A 1582 PHE cc_start: 0.9433 (m-80) cc_final: 0.9073 (m-80) REVERT: A 1587 HIS cc_start: 0.9264 (m-70) cc_final: 0.8905 (m90) REVERT: A 1653 ARG cc_start: 0.9367 (mtt180) cc_final: 0.9106 (ttm-80) REVERT: A 1656 MET cc_start: 0.8653 (tpt) cc_final: 0.8409 (tpt) REVERT: A 1740 VAL cc_start: 0.9577 (t) cc_final: 0.9282 (p) REVERT: A 2010 MET cc_start: 0.9458 (mmm) cc_final: 0.8911 (mmm) REVERT: A 2019 ASN cc_start: 0.8365 (m-40) cc_final: 0.7715 (m-40) REVERT: A 2091 LEU cc_start: 0.9452 (mt) cc_final: 0.9090 (mt) REVERT: A 2093 LEU cc_start: 0.9375 (mt) cc_final: 0.8852 (mt) REVERT: A 2097 TYR cc_start: 0.7970 (m-80) cc_final: 0.7677 (m-80) REVERT: A 2144 GLN cc_start: 0.9210 (mt0) cc_final: 0.8918 (mp10) REVERT: A 2162 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8634 (pp20) REVERT: A 2166 LYS cc_start: 0.9313 (mttt) cc_final: 0.8826 (ptmm) REVERT: A 2310 LYS cc_start: 0.9305 (mtmt) cc_final: 0.8755 (mppt) REVERT: A 2423 VAL cc_start: 0.9371 (t) cc_final: 0.9033 (p) REVERT: A 2436 PHE cc_start: 0.8549 (m-80) cc_final: 0.7966 (m-80) REVERT: A 2437 HIS cc_start: 0.8661 (t70) cc_final: 0.8296 (t70) REVERT: A 2464 MET cc_start: 0.8504 (tpt) cc_final: 0.8244 (tpt) REVERT: A 2489 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8127 (mt-10) REVERT: A 2515 LEU cc_start: 0.9544 (tp) cc_final: 0.9339 (tp) REVERT: A 2523 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7186 (pp-130) REVERT: A 2531 LEU cc_start: 0.9675 (mt) cc_final: 0.9442 (mt) REVERT: A 2534 ARG cc_start: 0.9023 (tpt170) cc_final: 0.8687 (tpp80) REVERT: A 2554 LEU cc_start: 0.9392 (mt) cc_final: 0.9161 (mt) REVERT: A 2595 ILE cc_start: 0.9762 (mt) cc_final: 0.9491 (mm) REVERT: A 2632 LEU cc_start: 0.9292 (tm) cc_final: 0.8672 (tt) REVERT: B 1575 GLN cc_start: 0.8778 (mt0) cc_final: 0.8346 (mp10) REVERT: B 1582 PHE cc_start: 0.9249 (m-80) cc_final: 0.8844 (m-80) REVERT: B 1584 MET cc_start: 0.8901 (mtm) cc_final: 0.8405 (mmp) REVERT: B 1702 LEU cc_start: 0.9081 (mt) cc_final: 0.8651 (tt) REVERT: B 1703 LYS cc_start: 0.9367 (mttt) cc_final: 0.8890 (ptpt) REVERT: B 1742 SER cc_start: 0.9762 (m) cc_final: 0.9540 (p) REVERT: B 1743 MET cc_start: 0.9453 (mmm) cc_final: 0.8849 (mmm) REVERT: B 1749 LEU cc_start: 0.9577 (mt) cc_final: 0.9020 (mt) REVERT: B 1826 VAL cc_start: 0.9524 (OUTLIER) cc_final: 0.9180 (p) REVERT: B 1889 MET cc_start: 0.7841 (mmm) cc_final: 0.7362 (mmm) REVERT: B 1901 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8243 (tm) REVERT: B 1942 ASN cc_start: 0.8955 (m-40) cc_final: 0.8578 (p0) REVERT: B 1951 ARG cc_start: 0.7191 (mpp80) cc_final: 0.6726 (ttp-110) REVERT: B 2010 MET cc_start: 0.8729 (mmm) cc_final: 0.8505 (mmm) REVERT: B 2024 LYS cc_start: 0.9220 (mttt) cc_final: 0.8948 (tttm) REVERT: B 2040 PHE cc_start: 0.7580 (p90) cc_final: 0.7288 (p90) REVERT: B 2052 MET cc_start: 0.9223 (mmm) cc_final: 0.8848 (mmp) REVERT: B 2069 VAL cc_start: 0.9537 (t) cc_final: 0.9256 (m) REVERT: B 2074 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7569 (mtp85) REVERT: B 2084 TYR cc_start: 0.7684 (t80) cc_final: 0.7426 (t80) REVERT: B 2094 TRP cc_start: 0.8079 (m100) cc_final: 0.7555 (m100) REVERT: B 2129 HIS cc_start: 0.8543 (t70) cc_final: 0.8178 (t-170) REVERT: B 2132 TYR cc_start: 0.9031 (m-80) cc_final: 0.8477 (m-80) REVERT: B 2140 THR cc_start: 0.8842 (p) cc_final: 0.8633 (p) REVERT: B 2206 LYS cc_start: 0.9062 (mttt) cc_final: 0.8669 (ptpp) REVERT: B 2324 MET cc_start: 0.9446 (mmm) cc_final: 0.8943 (mmm) REVERT: B 2338 LEU cc_start: 0.9662 (mt) cc_final: 0.9334 (mt) REVERT: B 2347 LYS cc_start: 0.9405 (mttt) cc_final: 0.8905 (mmmt) REVERT: B 2349 LEU cc_start: 0.9698 (mt) cc_final: 0.9340 (mp) REVERT: B 2356 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7443 (mmm160) REVERT: B 2376 ILE cc_start: 0.9044 (mt) cc_final: 0.8505 (mm) REVERT: B 2407 ARG cc_start: 0.8825 (mtt180) cc_final: 0.8599 (tpt90) REVERT: B 2438 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8717 (mt-10) REVERT: B 2531 LEU cc_start: 0.9068 (mt) cc_final: 0.8840 (tt) REVERT: B 2593 LEU cc_start: 0.9461 (mt) cc_final: 0.9035 (mm) REVERT: B 2597 GLN cc_start: 0.9174 (mp10) cc_final: 0.8950 (mp10) REVERT: B 2629 ASP cc_start: 0.7684 (m-30) cc_final: 0.7465 (m-30) outliers start: 18 outliers final: 2 residues processed: 653 average time/residue: 0.2236 time to fit residues: 228.3172 Evaluate side-chains 453 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 448 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 chunk 265 optimal weight: 30.0000 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 40.0000 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 0.6980 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1672 HIS A1755 GLN ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1936 HIS A1937 HIS A1971 GLN A2019 ASN ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2123 ASN ** A2151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2432 HIS ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2496 ASN A2517 HIS ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1672 HIS B1771 ASN ** B1830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1845 GLN B1936 HIS ** B1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1971 GLN B1987 ASN ** B2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2019 ASN ** B2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2280 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2591 HIS B2635 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.073225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.053237 restraints weight = 194703.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.055077 restraints weight = 115010.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.056363 restraints weight = 78633.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.057311 restraints weight = 59191.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058002 restraints weight = 47687.448| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 33739 Z= 0.237 Angle : 0.898 11.133 46280 Z= 0.498 Chirality : 0.047 0.262 5753 Planarity : 0.006 0.113 6264 Dihedral : 9.428 64.365 5588 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.10 % Favored : 84.15 % Rotamer: Outliers : 0.27 % Allowed : 3.95 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 4.72 % Twisted General : 1.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.24 (0.10), residues: 5364 helix: -2.20 (0.07), residues: 3547 sheet: -3.33 (0.60), residues: 57 loop : -3.87 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2074 TYR 0.038 0.002 TYR A2394 PHE 0.030 0.002 PHE A2436 TRP 0.028 0.003 TRP A2104 HIS 0.011 0.002 HIS A1709 Details of bonding type rmsd covalent geometry : bond 0.00440 (33737) covalent geometry : angle 0.89564 (46276) SS BOND : bond 0.00721 ( 2) SS BOND : angle 7.03731 ( 4) hydrogen bonds : bond 0.07545 ( 2089) hydrogen bonds : angle 7.40112 ( 6177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 561 time to evaluate : 1.212 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: A 1537 LEU cc_start: 0.9418 (mt) cc_final: 0.9184 (mt) REVERT: A 1582 PHE cc_start: 0.9293 (m-80) cc_final: 0.8895 (m-80) REVERT: A 1664 GLU cc_start: 0.8839 (tp30) cc_final: 0.8635 (tp30) REVERT: A 1665 LYS cc_start: 0.9362 (mttt) cc_final: 0.8829 (mttt) REVERT: A 1743 MET cc_start: 0.9498 (mtm) cc_final: 0.9133 (mtp) REVERT: A 1929 ARG cc_start: 0.9305 (mtt180) cc_final: 0.8681 (mtt-85) REVERT: A 1932 ARG cc_start: 0.8574 (mtt90) cc_final: 0.8374 (mtt-85) REVERT: A 1938 GLN cc_start: 0.8119 (mt0) cc_final: 0.7874 (mt0) REVERT: A 2003 MET cc_start: 0.8752 (tpt) cc_final: 0.8470 (tpp) REVERT: A 2010 MET cc_start: 0.9343 (mmm) cc_final: 0.8890 (mmm) REVERT: A 2024 LYS cc_start: 0.9224 (tmmt) cc_final: 0.8796 (mmmt) REVERT: A 2074 ARG cc_start: 0.8492 (mtp85) cc_final: 0.7321 (ptm160) REVERT: A 2093 LEU cc_start: 0.9539 (mt) cc_final: 0.8924 (mt) REVERT: A 2097 TYR cc_start: 0.8400 (m-80) cc_final: 0.7889 (m-80) REVERT: A 2100 LYS cc_start: 0.9341 (mttt) cc_final: 0.9063 (mmmt) REVERT: A 2115 MET cc_start: 0.9066 (mmp) cc_final: 0.8769 (mmm) REVERT: A 2155 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8347 (tp30) REVERT: A 2166 LYS cc_start: 0.9184 (mttt) cc_final: 0.8809 (ptmm) REVERT: A 2179 MET cc_start: 0.9182 (mmp) cc_final: 0.8962 (mmm) REVERT: A 2310 LYS cc_start: 0.9479 (mtmt) cc_final: 0.8969 (mppt) REVERT: A 2325 MET cc_start: 0.7733 (mmm) cc_final: 0.7507 (mmp) REVERT: A 2338 LEU cc_start: 0.9688 (mp) cc_final: 0.9390 (mp) REVERT: A 2339 MET cc_start: 0.9270 (mmt) cc_final: 0.8734 (mmt) REVERT: A 2422 LYS cc_start: 0.9721 (mmtp) cc_final: 0.9514 (mttt) REVERT: A 2429 LEU cc_start: 0.9459 (mt) cc_final: 0.8956 (tp) REVERT: A 2437 HIS cc_start: 0.8593 (t70) cc_final: 0.8235 (t70) REVERT: A 2458 CYS cc_start: 0.9670 (m) cc_final: 0.9302 (p) REVERT: A 2464 MET cc_start: 0.9107 (tpt) cc_final: 0.8870 (tpt) REVERT: A 2466 MET cc_start: 0.9213 (mmp) cc_final: 0.9003 (mmp) REVERT: A 2467 VAL cc_start: 0.9388 (t) cc_final: 0.8950 (p) REVERT: A 2531 LEU cc_start: 0.9613 (mt) cc_final: 0.9324 (mt) REVERT: A 2539 THR cc_start: 0.9791 (p) cc_final: 0.9388 (p) REVERT: B 1575 GLN cc_start: 0.8844 (mt0) cc_final: 0.8457 (mp10) REVERT: B 1582 PHE cc_start: 0.9481 (m-80) cc_final: 0.8917 (m-80) REVERT: B 1584 MET cc_start: 0.9283 (mtm) cc_final: 0.8900 (mmp) REVERT: B 1703 LYS cc_start: 0.9134 (mttt) cc_final: 0.8863 (ptpt) REVERT: B 1743 MET cc_start: 0.9410 (mmm) cc_final: 0.9189 (mmm) REVERT: B 1841 ARG cc_start: 0.9188 (mmm-85) cc_final: 0.8947 (tpp80) REVERT: B 1889 MET cc_start: 0.8222 (mmm) cc_final: 0.7585 (mmm) REVERT: B 1932 ARG cc_start: 0.8617 (mtt90) cc_final: 0.8406 (mtt-85) REVERT: B 1942 ASN cc_start: 0.8780 (m-40) cc_final: 0.8579 (p0) REVERT: B 1961 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8506 (mmtt) REVERT: B 1962 TRP cc_start: 0.8487 (t60) cc_final: 0.8143 (t60) REVERT: B 1996 MET cc_start: 0.9083 (mpp) cc_final: 0.8561 (mpp) REVERT: B 2019 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.7164 (t0) REVERT: B 2040 PHE cc_start: 0.7941 (p90) cc_final: 0.7520 (p90) REVERT: B 2052 MET cc_start: 0.9208 (mmm) cc_final: 0.8664 (mmp) REVERT: B 2055 ASP cc_start: 0.9624 (m-30) cc_final: 0.9324 (m-30) REVERT: B 2069 VAL cc_start: 0.9106 (t) cc_final: 0.8906 (t) REVERT: B 2074 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7235 (mtp85) REVERT: B 2094 TRP cc_start: 0.8327 (m100) cc_final: 0.7928 (m100) REVERT: B 2132 TYR cc_start: 0.9124 (m-80) cc_final: 0.8651 (m-80) REVERT: B 2206 LYS cc_start: 0.9255 (mttt) cc_final: 0.8922 (ptpp) REVERT: B 2333 ARG cc_start: 0.9067 (tpt-90) cc_final: 0.8766 (mmm-85) REVERT: B 2338 LEU cc_start: 0.9486 (mt) cc_final: 0.9283 (mt) REVERT: B 2340 GLU cc_start: 0.9162 (pt0) cc_final: 0.8946 (pt0) REVERT: B 2347 LYS cc_start: 0.9224 (mttt) cc_final: 0.8921 (mmmt) REVERT: B 2376 ILE cc_start: 0.8905 (mt) cc_final: 0.8640 (mm) REVERT: B 2438 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8566 (mt-10) REVERT: B 2458 CYS cc_start: 0.9562 (m) cc_final: 0.9053 (p) REVERT: B 2489 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8490 (mt-10) REVERT: B 2505 PHE cc_start: 0.8805 (t80) cc_final: 0.8490 (t80) REVERT: B 2548 GLU cc_start: 0.9492 (mp0) cc_final: 0.9069 (mp0) REVERT: B 2594 ASP cc_start: 0.9229 (m-30) cc_final: 0.8905 (m-30) REVERT: B 2596 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9081 (mt-10) REVERT: B 2597 GLN cc_start: 0.9156 (mp10) cc_final: 0.8804 (mt0) REVERT: B 2633 LEU cc_start: 0.9223 (tt) cc_final: 0.9016 (mt) REVERT: B 2635 GLN cc_start: 0.9318 (mt0) cc_final: 0.8604 (tm-30) REVERT: B 2644 MET cc_start: 0.8306 (mmm) cc_final: 0.7378 (mmm) outliers start: 5 outliers final: 0 residues processed: 564 average time/residue: 0.2074 time to fit residues: 187.5880 Evaluate side-chains 428 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 320 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 449 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 474 optimal weight: 0.8980 chunk 67 optimal weight: 40.0000 chunk 268 optimal weight: 1.9990 chunk 416 optimal weight: 0.0370 chunk 113 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1531 HIS A1735 HIS A1737 HIS ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 ASN ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2559 HIS A2591 HIS A2597 GLN ** A2625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1748 GLN B1771 ASN ** B1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1938 GLN ** B1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2015 ASN ** B2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2518 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.076514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.056088 restraints weight = 181623.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.058050 restraints weight = 108849.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059420 restraints weight = 74810.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.060410 restraints weight = 56477.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.061153 restraints weight = 45456.448| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33739 Z= 0.168 Angle : 0.778 11.048 46280 Z= 0.424 Chirality : 0.045 0.233 5753 Planarity : 0.005 0.105 6264 Dihedral : 8.257 61.998 5588 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.08 % Favored : 85.38 % Rotamer: Outliers : 0.32 % Allowed : 4.49 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.86 % Twisted General : 0.70 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.15 (0.11), residues: 5364 helix: -1.28 (0.08), residues: 3611 sheet: -2.91 (0.61), residues: 57 loop : -3.72 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B2350 TYR 0.032 0.002 TYR A2394 PHE 0.029 0.002 PHE A2436 TRP 0.050 0.003 TRP A2104 HIS 0.011 0.002 HIS A1862 Details of bonding type rmsd covalent geometry : bond 0.00335 (33737) covalent geometry : angle 0.77728 (46276) SS BOND : bond 0.00378 ( 2) SS BOND : angle 4.10652 ( 4) hydrogen bonds : bond 0.05060 ( 2089) hydrogen bonds : angle 6.32206 ( 6177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 551 time to evaluate : 1.211 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: A 1537 LEU cc_start: 0.9392 (mt) cc_final: 0.9176 (mt) REVERT: A 1582 PHE cc_start: 0.9239 (m-80) cc_final: 0.8807 (m-80) REVERT: A 1663 THR cc_start: 0.8659 (p) cc_final: 0.8063 (p) REVERT: A 1664 GLU cc_start: 0.8932 (tp30) cc_final: 0.8597 (tp30) REVERT: A 1665 LYS cc_start: 0.9226 (mttt) cc_final: 0.8880 (mttt) REVERT: A 1737 HIS cc_start: 0.8812 (t70) cc_final: 0.8598 (t70) REVERT: A 1741 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8927 (mmmm) REVERT: A 1743 MET cc_start: 0.9500 (mtm) cc_final: 0.9183 (mtp) REVERT: A 1946 ASN cc_start: 0.9312 (t0) cc_final: 0.8800 (t0) REVERT: A 1964 TRP cc_start: 0.8294 (t60) cc_final: 0.8077 (t60) REVERT: A 1976 LEU cc_start: 0.9397 (mt) cc_final: 0.9064 (mt) REVERT: A 2003 MET cc_start: 0.8637 (tpt) cc_final: 0.8409 (tpp) REVERT: A 2022 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8732 (mtt) REVERT: A 2058 MET cc_start: 0.8348 (ptm) cc_final: 0.7443 (ppp) REVERT: A 2089 ARG cc_start: 0.8679 (mtt180) cc_final: 0.8463 (mtt180) REVERT: A 2093 LEU cc_start: 0.9404 (mt) cc_final: 0.8934 (mt) REVERT: A 2097 TYR cc_start: 0.8538 (m-80) cc_final: 0.8084 (m-80) REVERT: A 2099 THR cc_start: 0.9389 (p) cc_final: 0.9131 (p) REVERT: A 2100 LYS cc_start: 0.9373 (mttt) cc_final: 0.8907 (mmtm) REVERT: A 2140 THR cc_start: 0.8944 (t) cc_final: 0.7601 (t) REVERT: A 2151 HIS cc_start: 0.7244 (m-70) cc_final: 0.5983 (m-70) REVERT: A 2155 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8550 (tp30) REVERT: A 2163 ILE cc_start: 0.9547 (mt) cc_final: 0.8979 (mt) REVERT: A 2166 LYS cc_start: 0.9232 (mttt) cc_final: 0.8837 (ptmm) REVERT: A 2178 MET cc_start: 0.9179 (mpp) cc_final: 0.8959 (mpp) REVERT: A 2179 MET cc_start: 0.9401 (mmp) cc_final: 0.9013 (mmm) REVERT: A 2223 LEU cc_start: 0.9433 (mt) cc_final: 0.9162 (tp) REVERT: A 2266 MET cc_start: 0.8675 (mmm) cc_final: 0.8324 (pmm) REVERT: A 2310 LYS cc_start: 0.9446 (mtmt) cc_final: 0.8874 (mppt) REVERT: A 2339 MET cc_start: 0.9191 (mmt) cc_final: 0.8383 (mmt) REVERT: A 2429 LEU cc_start: 0.9445 (mt) cc_final: 0.9053 (tp) REVERT: A 2437 HIS cc_start: 0.8448 (t70) cc_final: 0.7970 (t70) REVERT: A 2458 CYS cc_start: 0.9627 (m) cc_final: 0.9365 (p) REVERT: A 2464 MET cc_start: 0.9246 (tpt) cc_final: 0.8962 (tpt) REVERT: A 2466 MET cc_start: 0.9296 (mmp) cc_final: 0.8767 (ttp) REVERT: A 2482 LEU cc_start: 0.9057 (mm) cc_final: 0.8777 (mt) REVERT: A 2531 LEU cc_start: 0.9600 (mt) cc_final: 0.9303 (mt) REVERT: A 2597 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8620 (mp10) REVERT: A 2600 GLN cc_start: 0.9563 (mt0) cc_final: 0.9154 (mm-40) REVERT: A 2636 MET cc_start: 0.8708 (mmp) cc_final: 0.8491 (mmm) REVERT: B 1541 ASN cc_start: 0.9399 (t0) cc_final: 0.9117 (t0) REVERT: B 1575 GLN cc_start: 0.8890 (mt0) cc_final: 0.8529 (mp10) REVERT: B 1582 PHE cc_start: 0.9424 (m-80) cc_final: 0.9010 (m-80) REVERT: B 1651 TYR cc_start: 0.8360 (m-80) cc_final: 0.7911 (m-80) REVERT: B 1702 LEU cc_start: 0.9305 (tt) cc_final: 0.8921 (pt) REVERT: B 1703 LYS cc_start: 0.9074 (mttt) cc_final: 0.8767 (ptpt) REVERT: B 1889 MET cc_start: 0.8310 (mmm) cc_final: 0.7608 (mmm) REVERT: B 1932 ARG cc_start: 0.8626 (mtt90) cc_final: 0.8203 (mtt180) REVERT: B 1951 ARG cc_start: 0.7639 (ptt-90) cc_final: 0.7386 (pmt170) REVERT: B 1961 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8385 (mmtt) REVERT: B 1962 TRP cc_start: 0.8550 (t60) cc_final: 0.8223 (t60) REVERT: B 1996 MET cc_start: 0.8743 (mpp) cc_final: 0.8316 (pmm) REVERT: B 2040 PHE cc_start: 0.7710 (p90) cc_final: 0.7168 (p90) REVERT: B 2052 MET cc_start: 0.9098 (mmm) cc_final: 0.8619 (mmp) REVERT: B 2055 ASP cc_start: 0.9622 (m-30) cc_final: 0.9370 (m-30) REVERT: B 2132 TYR cc_start: 0.9168 (m-80) cc_final: 0.8831 (m-80) REVERT: B 2179 MET cc_start: 0.9068 (tpp) cc_final: 0.8592 (tpp) REVERT: B 2206 LYS cc_start: 0.9259 (mttt) cc_final: 0.8866 (ptpp) REVERT: B 2333 ARG cc_start: 0.8940 (tpt-90) cc_final: 0.8698 (mmm-85) REVERT: B 2339 MET cc_start: 0.9367 (mmt) cc_final: 0.8558 (mmt) REVERT: B 2340 GLU cc_start: 0.9213 (pt0) cc_final: 0.8949 (pt0) REVERT: B 2376 ILE cc_start: 0.9179 (mt) cc_final: 0.8863 (mt) REVERT: B 2438 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8511 (mt-10) REVERT: B 2479 GLU cc_start: 0.8605 (tp30) cc_final: 0.8399 (mm-30) REVERT: B 2489 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8686 (mt-10) REVERT: B 2505 PHE cc_start: 0.8974 (t80) cc_final: 0.8615 (t80) REVERT: B 2546 GLN cc_start: 0.8015 (mp10) cc_final: 0.7722 (mp10) REVERT: B 2597 GLN cc_start: 0.9164 (mp10) cc_final: 0.8939 (mt0) REVERT: B 2620 VAL cc_start: 0.9351 (t) cc_final: 0.9135 (t) outliers start: 6 outliers final: 1 residues processed: 555 average time/residue: 0.1953 time to fit residues: 176.3068 Evaluate side-chains 438 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 435 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 352 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 chunk 249 optimal weight: 20.0000 chunk 178 optimal weight: 0.0470 chunk 492 optimal weight: 4.9990 chunk 431 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 489 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 258 optimal weight: 20.0000 chunk 533 optimal weight: 5.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2081 GLN ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2361 HIS ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2597 GLN ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1735 HIS B1771 ASN ** B1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2019 ASN B2056 ASN ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2342 ASN B2361 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.072944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.053138 restraints weight = 189727.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054936 restraints weight = 116215.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056180 restraints weight = 80457.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057016 restraints weight = 61308.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.057700 restraints weight = 50223.640| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 33739 Z= 0.253 Angle : 0.807 12.660 46280 Z= 0.446 Chirality : 0.045 0.205 5753 Planarity : 0.005 0.103 6264 Dihedral : 7.997 63.165 5588 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.52 % Allowed : 15.19 % Favored : 84.28 % Rotamer: Outliers : 0.11 % Allowed : 3.90 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.86 % Twisted General : 0.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.11), residues: 5364 helix: -0.71 (0.08), residues: 3620 sheet: -2.91 (0.64), residues: 57 loop : -3.58 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B2541 TYR 0.029 0.002 TYR A2394 PHE 0.036 0.002 PHE A2016 TRP 0.042 0.003 TRP A2104 HIS 0.014 0.002 HIS A2492 Details of bonding type rmsd covalent geometry : bond 0.00483 (33737) covalent geometry : angle 0.80682 (46276) SS BOND : bond 0.00874 ( 2) SS BOND : angle 2.51010 ( 4) hydrogen bonds : bond 0.04919 ( 2089) hydrogen bonds : angle 6.05615 ( 6177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 489 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1582 PHE cc_start: 0.9285 (m-80) cc_final: 0.8878 (m-80) REVERT: A 1683 MET cc_start: 0.8750 (mmm) cc_final: 0.8116 (mmm) REVERT: A 1699 GLU cc_start: 0.8908 (mp0) cc_final: 0.8690 (pm20) REVERT: A 1737 HIS cc_start: 0.9007 (t70) cc_final: 0.8451 (t-90) REVERT: A 1854 LEU cc_start: 0.9404 (mm) cc_final: 0.8868 (mm) REVERT: A 1856 MET cc_start: 0.9353 (mtp) cc_final: 0.9145 (mtp) REVERT: A 1916 TYR cc_start: 0.8338 (p90) cc_final: 0.8117 (p90) REVERT: A 1951 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7461 (ptp-170) REVERT: A 1976 LEU cc_start: 0.9376 (mt) cc_final: 0.9161 (mm) REVERT: A 2003 MET cc_start: 0.8641 (tpt) cc_final: 0.8398 (tpp) REVERT: A 2009 PHE cc_start: 0.7457 (m-80) cc_final: 0.7219 (m-80) REVERT: A 2034 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8914 (mp0) REVERT: A 2058 MET cc_start: 0.8210 (ptm) cc_final: 0.7440 (ppp) REVERT: A 2078 TYR cc_start: 0.8565 (t80) cc_final: 0.8334 (t80) REVERT: A 2089 ARG cc_start: 0.9118 (mtt180) cc_final: 0.8798 (mtt180) REVERT: A 2093 LEU cc_start: 0.9537 (mt) cc_final: 0.8828 (mt) REVERT: A 2097 TYR cc_start: 0.8581 (m-80) cc_final: 0.8335 (m-80) REVERT: A 2099 THR cc_start: 0.9492 (p) cc_final: 0.8273 (p) REVERT: A 2100 LYS cc_start: 0.9341 (mttt) cc_final: 0.8982 (mmtp) REVERT: A 2115 MET cc_start: 0.9082 (mmp) cc_final: 0.8710 (mmm) REVERT: A 2166 LYS cc_start: 0.9262 (mttt) cc_final: 0.8950 (ptmm) REVERT: A 2178 MET cc_start: 0.9051 (mpp) cc_final: 0.8829 (mpp) REVERT: A 2179 MET cc_start: 0.9383 (mmp) cc_final: 0.9104 (mmm) REVERT: A 2225 LEU cc_start: 0.9538 (mt) cc_final: 0.9332 (mt) REVERT: A 2270 LEU cc_start: 0.9452 (mt) cc_final: 0.8681 (mt) REVERT: A 2310 LYS cc_start: 0.9378 (mtmt) cc_final: 0.8919 (mppt) REVERT: A 2324 MET cc_start: 0.8630 (tpp) cc_final: 0.8410 (tpp) REVERT: A 2339 MET cc_start: 0.9111 (mmt) cc_final: 0.8423 (mmt) REVERT: A 2429 LEU cc_start: 0.9460 (mt) cc_final: 0.8984 (tp) REVERT: A 2437 HIS cc_start: 0.8833 (t70) cc_final: 0.8386 (t70) REVERT: A 2458 CYS cc_start: 0.9670 (m) cc_final: 0.9272 (t) REVERT: A 2466 MET cc_start: 0.9241 (mmp) cc_final: 0.9000 (mmp) REVERT: A 2519 MET cc_start: 0.9272 (mtp) cc_final: 0.9050 (mtp) REVERT: A 2531 LEU cc_start: 0.9598 (mt) cc_final: 0.9266 (mt) REVERT: A 2612 LEU cc_start: 0.9473 (mp) cc_final: 0.9228 (tt) REVERT: A 2636 MET cc_start: 0.8828 (mmp) cc_final: 0.8626 (mmm) REVERT: B 1541 ASN cc_start: 0.9402 (t0) cc_final: 0.9033 (t0) REVERT: B 1575 GLN cc_start: 0.8924 (mt0) cc_final: 0.8553 (mp10) REVERT: B 1582 PHE cc_start: 0.9472 (m-80) cc_final: 0.9045 (m-80) REVERT: B 1584 MET cc_start: 0.9456 (mtt) cc_final: 0.9150 (mmm) REVERT: B 1651 TYR cc_start: 0.8284 (m-80) cc_final: 0.7843 (m-80) REVERT: B 1673 LEU cc_start: 0.9282 (tp) cc_final: 0.8970 (tt) REVERT: B 1703 LYS cc_start: 0.9274 (mttt) cc_final: 0.8944 (ptpt) REVERT: B 1776 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8749 (mt-10) REVERT: B 1933 LYS cc_start: 0.9648 (mttt) cc_final: 0.9388 (mmmt) REVERT: B 1961 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8454 (mmtt) REVERT: B 1962 TRP cc_start: 0.8474 (t60) cc_final: 0.7942 (t60) REVERT: B 1964 TRP cc_start: 0.8263 (t60) cc_final: 0.7966 (t60) REVERT: B 1996 MET cc_start: 0.8842 (mpp) cc_final: 0.8512 (pmm) REVERT: B 2003 MET cc_start: 0.8689 (tpt) cc_final: 0.8300 (tpt) REVERT: B 2040 PHE cc_start: 0.7894 (p90) cc_final: 0.7449 (p90) REVERT: B 2047 ASP cc_start: 0.9124 (t0) cc_final: 0.8923 (t0) REVERT: B 2052 MET cc_start: 0.9121 (mmm) cc_final: 0.8641 (mmp) REVERT: B 2074 ARG cc_start: 0.8259 (mtp180) cc_final: 0.8017 (mtp85) REVERT: B 2094 TRP cc_start: 0.8356 (m100) cc_final: 0.8123 (m100) REVERT: B 2097 TYR cc_start: 0.7088 (m-80) cc_final: 0.6439 (m-80) REVERT: B 2100 LYS cc_start: 0.9440 (mttt) cc_final: 0.9208 (mmtt) REVERT: B 2179 MET cc_start: 0.8998 (tpp) cc_final: 0.8710 (tpp) REVERT: B 2189 MET cc_start: 0.9060 (ttt) cc_final: 0.8760 (tmm) REVERT: B 2206 LYS cc_start: 0.9255 (mttt) cc_final: 0.8959 (ptpp) REVERT: B 2339 MET cc_start: 0.9384 (mmt) cc_final: 0.8647 (mmt) REVERT: B 2356 ARG cc_start: 0.8393 (mtt180) cc_final: 0.7637 (mtp85) REVERT: B 2376 ILE cc_start: 0.9225 (mt) cc_final: 0.8947 (mt) REVERT: B 2407 ARG cc_start: 0.9127 (mtt180) cc_final: 0.8680 (tpt170) REVERT: B 2438 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8471 (mp0) REVERT: B 2479 GLU cc_start: 0.8650 (tp30) cc_final: 0.8448 (mm-30) REVERT: B 2529 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7682 (mp0) REVERT: B 2548 GLU cc_start: 0.9415 (mp0) cc_final: 0.9094 (pm20) REVERT: B 2597 GLN cc_start: 0.8882 (mp10) cc_final: 0.8414 (mt0) REVERT: B 2633 LEU cc_start: 0.8826 (tt) cc_final: 0.8562 (mt) outliers start: 2 outliers final: 0 residues processed: 491 average time/residue: 0.1959 time to fit residues: 156.5836 Evaluate side-chains 395 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 512 optimal weight: 0.0000 chunk 117 optimal weight: 20.0000 chunk 470 optimal weight: 5.9990 chunk 414 optimal weight: 0.0770 chunk 258 optimal weight: 3.9990 chunk 325 optimal weight: 30.0000 chunk 324 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 chunk 434 optimal weight: 7.9990 chunk 13 optimal weight: 40.0000 chunk 195 optimal weight: 1.9990 overall best weight: 1.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1936 HIS ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 ASN ** A2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2019 ASN ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2342 ASN ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2517 HIS B2546 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.075445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.055140 restraints weight = 183942.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057055 restraints weight = 110221.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058389 restraints weight = 76100.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059372 restraints weight = 57667.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.060087 restraints weight = 46606.227| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33739 Z= 0.151 Angle : 0.728 9.892 46280 Z= 0.396 Chirality : 0.044 0.200 5753 Planarity : 0.005 0.104 6264 Dihedral : 7.628 63.618 5588 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.08 % Favored : 85.40 % Rotamer: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.43 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.12), residues: 5364 helix: -0.21 (0.09), residues: 3619 sheet: -2.86 (0.66), residues: 57 loop : -3.52 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B2333 TYR 0.028 0.002 TYR A2394 PHE 0.037 0.002 PHE A2016 TRP 0.048 0.003 TRP A2104 HIS 0.011 0.001 HIS A2151 Details of bonding type rmsd covalent geometry : bond 0.00303 (33737) covalent geometry : angle 0.72761 (46276) SS BOND : bond 0.01934 ( 2) SS BOND : angle 3.35854 ( 4) hydrogen bonds : bond 0.04222 ( 2089) hydrogen bonds : angle 5.68389 ( 6177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 496 time to evaluate : 0.991 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: A 1537 LEU cc_start: 0.9347 (mt) cc_final: 0.9140 (mt) REVERT: A 1582 PHE cc_start: 0.9217 (m-80) cc_final: 0.8758 (m-80) REVERT: A 1664 GLU cc_start: 0.8994 (tp30) cc_final: 0.8701 (tm-30) REVERT: A 1665 LYS cc_start: 0.8824 (pttm) cc_final: 0.7938 (pttm) REVERT: A 1683 MET cc_start: 0.8626 (mmm) cc_final: 0.8059 (mmm) REVERT: A 1699 GLU cc_start: 0.8816 (mp0) cc_final: 0.8488 (pm20) REVERT: A 1737 HIS cc_start: 0.8855 (t70) cc_final: 0.8317 (t70) REVERT: A 1743 MET cc_start: 0.9417 (mtm) cc_final: 0.8954 (ptp) REVERT: A 1854 LEU cc_start: 0.9549 (mm) cc_final: 0.9022 (mm) REVERT: A 1946 ASN cc_start: 0.9535 (t0) cc_final: 0.9230 (t0) REVERT: A 1951 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7325 (ptt-90) REVERT: A 2011 GLU cc_start: 0.8665 (pp20) cc_final: 0.8371 (tm-30) REVERT: A 2026 LYS cc_start: 0.9712 (mttp) cc_final: 0.9454 (mmmt) REVERT: A 2058 MET cc_start: 0.8115 (ptm) cc_final: 0.7094 (ppp) REVERT: A 2078 TYR cc_start: 0.8542 (t80) cc_final: 0.8292 (t80) REVERT: A 2089 ARG cc_start: 0.9042 (mtt180) cc_final: 0.8676 (mtt180) REVERT: A 2093 LEU cc_start: 0.9489 (mt) cc_final: 0.8871 (mt) REVERT: A 2097 TYR cc_start: 0.8413 (m-10) cc_final: 0.8038 (m-80) REVERT: A 2099 THR cc_start: 0.9201 (p) cc_final: 0.8531 (p) REVERT: A 2100 LYS cc_start: 0.9309 (mttt) cc_final: 0.8733 (mmtm) REVERT: A 2140 THR cc_start: 0.8991 (t) cc_final: 0.8464 (t) REVERT: A 2151 HIS cc_start: 0.7615 (m-70) cc_final: 0.6501 (m90) REVERT: A 2155 GLU cc_start: 0.8911 (tp30) cc_final: 0.8560 (tp30) REVERT: A 2166 LYS cc_start: 0.9219 (mttt) cc_final: 0.8938 (ptmm) REVERT: A 2178 MET cc_start: 0.9176 (mpp) cc_final: 0.8938 (mpp) REVERT: A 2266 MET cc_start: 0.8580 (mmm) cc_final: 0.8238 (pmm) REVERT: A 2310 LYS cc_start: 0.9401 (mtmt) cc_final: 0.8955 (mppt) REVERT: A 2339 MET cc_start: 0.9109 (mmt) cc_final: 0.8356 (mmt) REVERT: A 2429 LEU cc_start: 0.9457 (mt) cc_final: 0.8981 (tp) REVERT: A 2437 HIS cc_start: 0.8899 (t70) cc_final: 0.8474 (t70) REVERT: A 2441 LEU cc_start: 0.9579 (mt) cc_final: 0.9362 (mt) REVERT: A 2458 CYS cc_start: 0.9705 (m) cc_final: 0.9264 (t) REVERT: A 2464 MET cc_start: 0.9334 (tpt) cc_final: 0.8918 (tpt) REVERT: A 2466 MET cc_start: 0.9272 (mmp) cc_final: 0.9031 (mmp) REVERT: A 2469 TYR cc_start: 0.9505 (t80) cc_final: 0.9130 (t80) REVERT: A 2482 LEU cc_start: 0.9231 (mm) cc_final: 0.8883 (mt) REVERT: A 2489 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8596 (mt-10) REVERT: A 2519 MET cc_start: 0.9284 (mtp) cc_final: 0.9042 (mtp) REVERT: A 2523 MET cc_start: 0.7020 (ptt) cc_final: 0.6818 (ptt) REVERT: A 2531 LEU cc_start: 0.9589 (mt) cc_final: 0.9242 (mt) REVERT: A 2539 THR cc_start: 0.9723 (p) cc_final: 0.9495 (p) REVERT: B 1541 ASN cc_start: 0.9378 (t0) cc_final: 0.9161 (t0) REVERT: B 1575 GLN cc_start: 0.8892 (mt0) cc_final: 0.8556 (mp10) REVERT: B 1582 PHE cc_start: 0.9404 (m-80) cc_final: 0.9181 (m-80) REVERT: B 1584 MET cc_start: 0.9475 (mtt) cc_final: 0.9155 (mmm) REVERT: B 1683 MET cc_start: 0.8944 (mmm) cc_final: 0.8385 (tpp) REVERT: B 1703 LYS cc_start: 0.9218 (mttt) cc_final: 0.8893 (ptpt) REVERT: B 1769 GLU cc_start: 0.8463 (mp0) cc_final: 0.8196 (mp0) REVERT: B 1776 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8879 (mt-10) REVERT: B 1852 VAL cc_start: 0.9770 (t) cc_final: 0.9411 (m) REVERT: B 1856 MET cc_start: 0.8971 (mmp) cc_final: 0.8675 (mmm) REVERT: B 1932 ARG cc_start: 0.8560 (ppt170) cc_final: 0.8072 (ttp80) REVERT: B 1946 ASN cc_start: 0.9085 (t0) cc_final: 0.8801 (t0) REVERT: B 1961 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8444 (mmtt) REVERT: B 1962 TRP cc_start: 0.8499 (t60) cc_final: 0.7949 (t60) REVERT: B 1964 TRP cc_start: 0.8170 (t60) cc_final: 0.7884 (t60) REVERT: B 1996 MET cc_start: 0.8859 (mpp) cc_final: 0.8521 (pmm) REVERT: B 2003 MET cc_start: 0.8723 (tpt) cc_final: 0.8335 (tpt) REVERT: B 2040 PHE cc_start: 0.7723 (p90) cc_final: 0.7355 (p90) REVERT: B 2052 MET cc_start: 0.9096 (mmm) cc_final: 0.8681 (mmp) REVERT: B 2100 LYS cc_start: 0.9385 (mttt) cc_final: 0.9088 (mmmt) REVERT: B 2179 MET cc_start: 0.9097 (tpp) cc_final: 0.8803 (tpp) REVERT: B 2206 LYS cc_start: 0.9276 (mttt) cc_final: 0.8916 (ptpp) REVERT: B 2338 LEU cc_start: 0.9551 (mt) cc_final: 0.9288 (mt) REVERT: B 2339 MET cc_start: 0.9305 (mmt) cc_final: 0.8663 (mmt) REVERT: B 2356 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7061 (mtp85) REVERT: B 2364 THR cc_start: 0.9479 (p) cc_final: 0.8794 (p) REVERT: B 2390 LEU cc_start: 0.9520 (mt) cc_final: 0.9315 (mt) REVERT: B 2407 ARG cc_start: 0.9080 (mtt180) cc_final: 0.8573 (tpt90) REVERT: B 2438 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8557 (mt-10) REVERT: B 2479 GLU cc_start: 0.8573 (tp30) cc_final: 0.8342 (mm-30) REVERT: B 2505 PHE cc_start: 0.8932 (t80) cc_final: 0.8624 (t80) REVERT: B 2526 MET cc_start: 0.8599 (tpt) cc_final: 0.8214 (tpt) REVERT: B 2529 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7649 (mp0) REVERT: B 2597 GLN cc_start: 0.8846 (mp10) cc_final: 0.8273 (mp10) REVERT: B 2633 LEU cc_start: 0.8681 (tt) cc_final: 0.8466 (mt) outliers start: 1 outliers final: 0 residues processed: 497 average time/residue: 0.1887 time to fit residues: 154.3803 Evaluate side-chains 421 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 87 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 521 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 412 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 453 optimal weight: 3.9990 chunk 525 optimal weight: 0.0870 chunk 113 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2263 GLN ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2546 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.075459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.055181 restraints weight = 183593.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057071 restraints weight = 112054.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.058396 restraints weight = 77854.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.059357 restraints weight = 59036.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.060077 restraints weight = 47950.442| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33739 Z= 0.149 Angle : 0.709 10.993 46280 Z= 0.385 Chirality : 0.043 0.192 5753 Planarity : 0.005 0.098 6264 Dihedral : 7.318 62.345 5588 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.17 % Favored : 85.35 % Rotamer: Outliers : 0.05 % Allowed : 2.22 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 2.58 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.12), residues: 5364 helix: 0.14 (0.09), residues: 3662 sheet: -2.95 (0.64), residues: 59 loop : -3.63 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1932 TYR 0.053 0.002 TYR B2097 PHE 0.017 0.001 PHE B1582 TRP 0.050 0.002 TRP A2104 HIS 0.012 0.001 HIS B2129 Details of bonding type rmsd covalent geometry : bond 0.00301 (33737) covalent geometry : angle 0.70776 (46276) SS BOND : bond 0.01502 ( 2) SS BOND : angle 3.93955 ( 4) hydrogen bonds : bond 0.03944 ( 2089) hydrogen bonds : angle 5.40023 ( 6177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 486 time to evaluate : 1.245 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 1537 LEU cc_start: 0.9326 (mt) cc_final: 0.9119 (mt) REVERT: A 1582 PHE cc_start: 0.9236 (m-80) cc_final: 0.8746 (m-80) REVERT: A 1673 LEU cc_start: 0.9532 (mt) cc_final: 0.9287 (mt) REVERT: A 1683 MET cc_start: 0.8632 (mmm) cc_final: 0.8038 (mmm) REVERT: A 1699 GLU cc_start: 0.8814 (mp0) cc_final: 0.8446 (pm20) REVERT: A 1737 HIS cc_start: 0.8903 (t70) cc_final: 0.8295 (t70) REVERT: A 1946 ASN cc_start: 0.9600 (t0) cc_final: 0.9368 (t0) REVERT: A 1951 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7454 (mtt180) REVERT: A 2009 PHE cc_start: 0.7184 (m-80) cc_final: 0.6824 (m-80) REVERT: A 2011 GLU cc_start: 0.8685 (pp20) cc_final: 0.8306 (tm-30) REVERT: A 2026 LYS cc_start: 0.9752 (mttp) cc_final: 0.9453 (tptp) REVERT: A 2058 MET cc_start: 0.8103 (ptm) cc_final: 0.7038 (ppp) REVERT: A 2078 TYR cc_start: 0.8510 (t80) cc_final: 0.8269 (t80) REVERT: A 2090 MET cc_start: 0.8971 (mmp) cc_final: 0.8614 (mmp) REVERT: A 2093 LEU cc_start: 0.9440 (mt) cc_final: 0.8687 (mt) REVERT: A 2097 TYR cc_start: 0.8409 (m-10) cc_final: 0.8187 (m-80) REVERT: A 2099 THR cc_start: 0.9162 (p) cc_final: 0.8350 (p) REVERT: A 2100 LYS cc_start: 0.9344 (mttt) cc_final: 0.8751 (mmtm) REVERT: A 2138 PHE cc_start: 0.9236 (m-80) cc_final: 0.8902 (m-80) REVERT: A 2140 THR cc_start: 0.9001 (t) cc_final: 0.8374 (t) REVERT: A 2151 HIS cc_start: 0.7769 (m-70) cc_final: 0.6444 (m-70) REVERT: A 2155 GLU cc_start: 0.8940 (tp30) cc_final: 0.8222 (tp30) REVERT: A 2166 LYS cc_start: 0.9281 (mttt) cc_final: 0.8980 (ptmm) REVERT: A 2310 LYS cc_start: 0.9252 (mtmt) cc_final: 0.8902 (mppt) REVERT: A 2339 MET cc_start: 0.9088 (mmt) cc_final: 0.8375 (mmt) REVERT: A 2429 LEU cc_start: 0.9452 (mt) cc_final: 0.8978 (tp) REVERT: A 2437 HIS cc_start: 0.9080 (t70) cc_final: 0.8758 (t70) REVERT: A 2458 CYS cc_start: 0.9682 (m) cc_final: 0.9278 (t) REVERT: A 2464 MET cc_start: 0.9392 (tpt) cc_final: 0.9160 (tpp) REVERT: A 2466 MET cc_start: 0.9248 (mmp) cc_final: 0.8967 (mmp) REVERT: A 2482 LEU cc_start: 0.9229 (mm) cc_final: 0.8891 (mt) REVERT: A 2489 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8538 (mt-10) REVERT: A 2523 MET cc_start: 0.7018 (ptt) cc_final: 0.6744 (ptt) REVERT: A 2531 LEU cc_start: 0.9579 (mt) cc_final: 0.9269 (mt) REVERT: A 2537 GLU cc_start: 0.9091 (pt0) cc_final: 0.8710 (pt0) REVERT: A 2539 THR cc_start: 0.9704 (p) cc_final: 0.9469 (p) REVERT: A 2599 LEU cc_start: 0.9464 (mm) cc_final: 0.8887 (pp) REVERT: A 2636 MET cc_start: 0.8863 (mmp) cc_final: 0.8603 (mmm) REVERT: B 1541 ASN cc_start: 0.9340 (t0) cc_final: 0.9117 (t0) REVERT: B 1575 GLN cc_start: 0.8906 (mt0) cc_final: 0.8586 (mp10) REVERT: B 1582 PHE cc_start: 0.9366 (m-80) cc_final: 0.9118 (m-80) REVERT: B 1584 MET cc_start: 0.9464 (mtt) cc_final: 0.9216 (mmp) REVERT: B 1651 TYR cc_start: 0.8204 (m-80) cc_final: 0.7726 (m-80) REVERT: B 1703 LYS cc_start: 0.9179 (mttt) cc_final: 0.8877 (ptpt) REVERT: B 1769 GLU cc_start: 0.8490 (mp0) cc_final: 0.8172 (mp0) REVERT: B 1776 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8934 (mt-10) REVERT: B 1852 VAL cc_start: 0.9767 (t) cc_final: 0.9454 (m) REVERT: B 1856 MET cc_start: 0.8887 (mmp) cc_final: 0.8685 (mmm) REVERT: B 1932 ARG cc_start: 0.8416 (ppt170) cc_final: 0.8104 (ttp80) REVERT: B 1946 ASN cc_start: 0.9065 (t0) cc_final: 0.8821 (t0) REVERT: B 1961 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8345 (mmtt) REVERT: B 1962 TRP cc_start: 0.8237 (t60) cc_final: 0.7846 (t60) REVERT: B 1964 TRP cc_start: 0.8150 (t60) cc_final: 0.7905 (t60) REVERT: B 1996 MET cc_start: 0.8850 (mpp) cc_final: 0.8476 (pmm) REVERT: B 2003 MET cc_start: 0.8828 (tpt) cc_final: 0.7720 (tpp) REVERT: B 2040 PHE cc_start: 0.7829 (p90) cc_final: 0.7454 (p90) REVERT: B 2052 MET cc_start: 0.8976 (mmm) cc_final: 0.8555 (mmp) REVERT: B 2074 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7626 (mtp85) REVERT: B 2100 LYS cc_start: 0.9396 (mttt) cc_final: 0.9106 (mmmt) REVERT: B 2115 MET cc_start: 0.8653 (tpp) cc_final: 0.8099 (tpt) REVERT: B 2132 TYR cc_start: 0.9236 (m-80) cc_final: 0.8839 (m-80) REVERT: B 2179 MET cc_start: 0.9193 (tpp) cc_final: 0.8889 (tpp) REVERT: B 2206 LYS cc_start: 0.9271 (mttt) cc_final: 0.8898 (ptpp) REVERT: B 2338 LEU cc_start: 0.9534 (mt) cc_final: 0.9218 (mt) REVERT: B 2356 ARG cc_start: 0.8233 (mtt180) cc_final: 0.6985 (mtp85) REVERT: B 2376 ILE cc_start: 0.9123 (mt) cc_final: 0.8905 (mt) REVERT: B 2390 LEU cc_start: 0.9535 (mt) cc_final: 0.9188 (mt) REVERT: B 2407 ARG cc_start: 0.9018 (mtt180) cc_final: 0.8660 (tpt170) REVERT: B 2438 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8544 (mt-10) REVERT: B 2475 ASP cc_start: 0.7763 (t0) cc_final: 0.7480 (t0) REVERT: B 2494 ASP cc_start: 0.7854 (t70) cc_final: 0.7551 (t0) REVERT: B 2505 PHE cc_start: 0.8903 (t80) cc_final: 0.8622 (t80) REVERT: B 2526 MET cc_start: 0.8555 (tpt) cc_final: 0.8261 (tpt) REVERT: B 2529 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7654 (mp0) REVERT: B 2546 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8795 (mm110) REVERT: B 2551 MET cc_start: 0.9228 (tpt) cc_final: 0.8979 (tpt) REVERT: B 2597 GLN cc_start: 0.8861 (mp10) cc_final: 0.8545 (mt0) REVERT: B 2633 LEU cc_start: 0.8769 (tt) cc_final: 0.8542 (mt) outliers start: 1 outliers final: 0 residues processed: 487 average time/residue: 0.1945 time to fit residues: 154.8718 Evaluate side-chains 419 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 3 optimal weight: 50.0000 chunk 203 optimal weight: 5.9990 chunk 229 optimal weight: 0.5980 chunk 487 optimal weight: 10.0000 chunk 445 optimal weight: 7.9990 chunk 270 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 471 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1748 GLN ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1737 HIS ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2077 GLN B2203 HIS ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2500 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.073710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.053659 restraints weight = 189195.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055464 restraints weight = 115486.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.056729 restraints weight = 80618.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.057659 restraints weight = 61555.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058338 restraints weight = 50092.414| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33739 Z= 0.202 Angle : 0.742 9.824 46280 Z= 0.406 Chirality : 0.044 0.208 5753 Planarity : 0.005 0.099 6264 Dihedral : 7.270 62.209 5588 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.06 % Favored : 84.43 % Rotamer: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.12), residues: 5364 helix: 0.32 (0.09), residues: 3657 sheet: -3.04 (0.63), residues: 57 loop : -3.68 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1951 TYR 0.045 0.002 TYR B2097 PHE 0.022 0.002 PHE A2016 TRP 0.054 0.003 TRP A2104 HIS 0.009 0.002 HIS B2492 Details of bonding type rmsd covalent geometry : bond 0.00390 (33737) covalent geometry : angle 0.74127 (46276) SS BOND : bond 0.00666 ( 2) SS BOND : angle 4.08197 ( 4) hydrogen bonds : bond 0.04052 ( 2089) hydrogen bonds : angle 5.34657 ( 6177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 465 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1582 PHE cc_start: 0.9232 (m-80) cc_final: 0.8782 (m-80) REVERT: A 1584 MET cc_start: 0.8919 (mpp) cc_final: 0.8534 (mpp) REVERT: A 1673 LEU cc_start: 0.9572 (mt) cc_final: 0.9350 (mt) REVERT: A 1683 MET cc_start: 0.8714 (mmm) cc_final: 0.8097 (mmm) REVERT: A 1699 GLU cc_start: 0.8921 (mp0) cc_final: 0.8554 (pm20) REVERT: A 1737 HIS cc_start: 0.8829 (t70) cc_final: 0.8253 (t70) REVERT: A 2009 PHE cc_start: 0.7495 (m-80) cc_final: 0.7020 (m-80) REVERT: A 2011 GLU cc_start: 0.8616 (pp20) cc_final: 0.8331 (tm-30) REVERT: A 2019 ASN cc_start: 0.6536 (m110) cc_final: 0.6076 (m110) REVERT: A 2026 LYS cc_start: 0.9734 (mttp) cc_final: 0.9526 (mmmt) REVERT: A 2058 MET cc_start: 0.8202 (ptm) cc_final: 0.7198 (ppp) REVERT: A 2074 ARG cc_start: 0.8426 (mtp85) cc_final: 0.7213 (ptm160) REVERT: A 2078 TYR cc_start: 0.8640 (t80) cc_final: 0.8299 (t80) REVERT: A 2082 PHE cc_start: 0.7422 (t80) cc_final: 0.6762 (t80) REVERT: A 2089 ARG cc_start: 0.8726 (mtt180) cc_final: 0.8334 (mtt180) REVERT: A 2093 LEU cc_start: 0.9496 (mt) cc_final: 0.8735 (mt) REVERT: A 2097 TYR cc_start: 0.8538 (m-10) cc_final: 0.8242 (m-80) REVERT: A 2099 THR cc_start: 0.9201 (p) cc_final: 0.8417 (p) REVERT: A 2100 LYS cc_start: 0.9330 (mttt) cc_final: 0.8837 (mmtm) REVERT: A 2138 PHE cc_start: 0.9261 (m-80) cc_final: 0.8890 (m-80) REVERT: A 2151 HIS cc_start: 0.7779 (m-70) cc_final: 0.6352 (m-70) REVERT: A 2155 GLU cc_start: 0.9022 (tp30) cc_final: 0.8343 (tp30) REVERT: A 2166 LYS cc_start: 0.9277 (mttt) cc_final: 0.9040 (ptmm) REVERT: A 2179 MET cc_start: 0.9411 (mmp) cc_final: 0.9176 (mmm) REVERT: A 2266 MET cc_start: 0.8214 (tpp) cc_final: 0.7994 (pmm) REVERT: A 2310 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8826 (mppt) REVERT: A 2339 MET cc_start: 0.9099 (mmt) cc_final: 0.8386 (mmt) REVERT: A 2429 LEU cc_start: 0.9471 (mt) cc_final: 0.8977 (tp) REVERT: A 2437 HIS cc_start: 0.9177 (t70) cc_final: 0.8868 (t70) REVERT: A 2458 CYS cc_start: 0.9684 (m) cc_final: 0.9423 (t) REVERT: A 2464 MET cc_start: 0.9433 (tpt) cc_final: 0.9150 (tpp) REVERT: A 2466 MET cc_start: 0.9259 (mmp) cc_final: 0.9029 (mmp) REVERT: A 2505 PHE cc_start: 0.8322 (t80) cc_final: 0.7880 (t80) REVERT: A 2523 MET cc_start: 0.6862 (ptt) cc_final: 0.6559 (ptt) REVERT: A 2531 LEU cc_start: 0.9580 (mt) cc_final: 0.9256 (mt) REVERT: A 2537 GLU cc_start: 0.9114 (pt0) cc_final: 0.8719 (pt0) REVERT: A 2551 MET cc_start: 0.9070 (ppp) cc_final: 0.8799 (ppp) REVERT: A 2556 THR cc_start: 0.9551 (p) cc_final: 0.8983 (p) REVERT: A 2617 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8413 (tm-30) REVERT: A 2636 MET cc_start: 0.8924 (mmp) cc_final: 0.8638 (mmm) REVERT: B 1575 GLN cc_start: 0.8881 (mt0) cc_final: 0.8540 (mp10) REVERT: B 1582 PHE cc_start: 0.9407 (m-80) cc_final: 0.9179 (m-80) REVERT: B 1584 MET cc_start: 0.9506 (mtt) cc_final: 0.9192 (mmp) REVERT: B 1651 TYR cc_start: 0.8307 (m-80) cc_final: 0.7823 (m-80) REVERT: B 1703 LYS cc_start: 0.9148 (mttt) cc_final: 0.8815 (ptpt) REVERT: B 1769 GLU cc_start: 0.8645 (mp0) cc_final: 0.8099 (mp0) REVERT: B 1776 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8778 (mt-10) REVERT: B 1852 VAL cc_start: 0.9790 (t) cc_final: 0.9473 (m) REVERT: B 1856 MET cc_start: 0.8964 (mmp) cc_final: 0.8757 (mmm) REVERT: B 1961 LYS cc_start: 0.9064 (mtmt) cc_final: 0.8602 (mmtt) REVERT: B 1962 TRP cc_start: 0.8262 (t60) cc_final: 0.7809 (t60) REVERT: B 1964 TRP cc_start: 0.8243 (t60) cc_final: 0.7994 (t60) REVERT: B 1996 MET cc_start: 0.8901 (mpp) cc_final: 0.8561 (pmm) REVERT: B 2040 PHE cc_start: 0.7914 (p90) cc_final: 0.7458 (p90) REVERT: B 2052 MET cc_start: 0.9014 (mmm) cc_final: 0.8635 (mmp) REVERT: B 2074 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7868 (mtp85) REVERT: B 2100 LYS cc_start: 0.9380 (mttt) cc_final: 0.9150 (pttm) REVERT: B 2132 TYR cc_start: 0.9247 (m-80) cc_final: 0.8870 (m-80) REVERT: B 2179 MET cc_start: 0.9176 (tpp) cc_final: 0.8924 (tpp) REVERT: B 2206 LYS cc_start: 0.9358 (mttt) cc_final: 0.8928 (ptpp) REVERT: B 2338 LEU cc_start: 0.9567 (mt) cc_final: 0.9310 (mt) REVERT: B 2376 ILE cc_start: 0.9212 (mt) cc_final: 0.8998 (mt) REVERT: B 2407 ARG cc_start: 0.9038 (mtt180) cc_final: 0.8680 (tpt170) REVERT: B 2438 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8443 (mp0) REVERT: B 2475 ASP cc_start: 0.7890 (t0) cc_final: 0.7591 (t0) REVERT: B 2494 ASP cc_start: 0.7966 (t70) cc_final: 0.7712 (t0) REVERT: B 2505 PHE cc_start: 0.8912 (t80) cc_final: 0.8528 (t80) REVERT: B 2526 MET cc_start: 0.8477 (tpt) cc_final: 0.8113 (tpt) REVERT: B 2529 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7834 (mp0) REVERT: B 2551 MET cc_start: 0.9309 (tpt) cc_final: 0.9091 (tpt) REVERT: B 2597 GLN cc_start: 0.8870 (mp10) cc_final: 0.8382 (mp10) REVERT: B 2608 ARG cc_start: 0.7671 (mtt90) cc_final: 0.7002 (ttm170) REVERT: B 2612 LEU cc_start: 0.9550 (mt) cc_final: 0.9347 (mt) REVERT: B 2633 LEU cc_start: 0.8923 (tt) cc_final: 0.8631 (mt) outliers start: 1 outliers final: 0 residues processed: 466 average time/residue: 0.1895 time to fit residues: 145.8314 Evaluate side-chains 399 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 311 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 40.0000 chunk 522 optimal weight: 2.9990 chunk 354 optimal weight: 0.0370 chunk 519 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 347 optimal weight: 8.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1748 GLN ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2283 HIS ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2242 HIS ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.073956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053671 restraints weight = 185832.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.055488 restraints weight = 114118.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056759 restraints weight = 80095.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057699 restraints weight = 61453.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058311 restraints weight = 50075.781| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33739 Z= 0.186 Angle : 0.732 10.656 46280 Z= 0.398 Chirality : 0.044 0.205 5753 Planarity : 0.005 0.099 6264 Dihedral : 7.158 62.014 5588 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.67 % Favored : 84.84 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.00 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.12), residues: 5364 helix: 0.51 (0.09), residues: 3671 sheet: -3.26 (0.58), residues: 59 loop : -3.72 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2074 TYR 0.040 0.002 TYR B2097 PHE 0.019 0.002 PHE B1868 TRP 0.056 0.003 TRP A2104 HIS 0.017 0.002 HIS B2129 Details of bonding type rmsd covalent geometry : bond 0.00360 (33737) covalent geometry : angle 0.73061 (46276) SS BOND : bond 0.00066 ( 2) SS BOND : angle 4.01914 ( 4) hydrogen bonds : bond 0.03960 ( 2089) hydrogen bonds : angle 5.23908 ( 6177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 1.151 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: A 1582 PHE cc_start: 0.9237 (m-80) cc_final: 0.8780 (m-80) REVERT: A 1584 MET cc_start: 0.8929 (mpp) cc_final: 0.8575 (mpp) REVERT: A 1673 LEU cc_start: 0.9562 (mt) cc_final: 0.9285 (mt) REVERT: A 1683 MET cc_start: 0.8701 (mmm) cc_final: 0.8069 (mmm) REVERT: A 1699 GLU cc_start: 0.8886 (mp0) cc_final: 0.8536 (pm20) REVERT: A 1737 HIS cc_start: 0.8860 (t70) cc_final: 0.8202 (t70) REVERT: A 1946 ASN cc_start: 0.9615 (t0) cc_final: 0.9415 (t0) REVERT: A 2011 GLU cc_start: 0.8662 (pp20) cc_final: 0.8356 (tm-30) REVERT: A 2058 MET cc_start: 0.8201 (ptm) cc_final: 0.7309 (ppp) REVERT: A 2074 ARG cc_start: 0.8537 (mtp85) cc_final: 0.7246 (ptm160) REVERT: A 2078 TYR cc_start: 0.8653 (t80) cc_final: 0.8271 (t80) REVERT: A 2093 LEU cc_start: 0.9459 (mt) cc_final: 0.8661 (mt) REVERT: A 2097 TYR cc_start: 0.8531 (m-10) cc_final: 0.8192 (m-80) REVERT: A 2100 LYS cc_start: 0.9300 (mttt) cc_final: 0.9079 (mttt) REVERT: A 2138 PHE cc_start: 0.9250 (m-80) cc_final: 0.8786 (m-80) REVERT: A 2140 THR cc_start: 0.9000 (t) cc_final: 0.8278 (t) REVERT: A 2155 GLU cc_start: 0.9062 (tp30) cc_final: 0.8370 (tp30) REVERT: A 2166 LYS cc_start: 0.9234 (mttt) cc_final: 0.9030 (ptmm) REVERT: A 2179 MET cc_start: 0.9438 (mmp) cc_final: 0.9166 (mmm) REVERT: A 2266 MET cc_start: 0.8127 (tpp) cc_final: 0.7876 (pmm) REVERT: A 2339 MET cc_start: 0.9137 (mmt) cc_final: 0.8464 (mmt) REVERT: A 2429 LEU cc_start: 0.9486 (mt) cc_final: 0.9000 (tp) REVERT: A 2437 HIS cc_start: 0.9204 (t70) cc_final: 0.8883 (t70) REVERT: A 2458 CYS cc_start: 0.9677 (m) cc_final: 0.9328 (t) REVERT: A 2464 MET cc_start: 0.9460 (tpt) cc_final: 0.9238 (tpp) REVERT: A 2466 MET cc_start: 0.9270 (mmp) cc_final: 0.9046 (mmp) REVERT: A 2505 PHE cc_start: 0.8417 (t80) cc_final: 0.7622 (t80) REVERT: A 2519 MET cc_start: 0.9225 (mtp) cc_final: 0.8995 (mtp) REVERT: A 2523 MET cc_start: 0.7131 (ptt) cc_final: 0.6915 (ptt) REVERT: A 2531 LEU cc_start: 0.9564 (mt) cc_final: 0.9235 (mt) REVERT: A 2537 GLU cc_start: 0.9158 (pt0) cc_final: 0.8747 (pt0) REVERT: A 2551 MET cc_start: 0.9087 (ppp) cc_final: 0.8719 (ppp) REVERT: A 2599 LEU cc_start: 0.9466 (mm) cc_final: 0.8885 (pp) REVERT: A 2600 GLN cc_start: 0.9606 (mt0) cc_final: 0.9322 (tt0) REVERT: A 2617 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 2636 MET cc_start: 0.8881 (mmp) cc_final: 0.8614 (mmm) REVERT: B 1553 MET cc_start: 0.8577 (mpp) cc_final: 0.8308 (mpp) REVERT: B 1575 GLN cc_start: 0.8927 (mt0) cc_final: 0.8529 (mp10) REVERT: B 1582 PHE cc_start: 0.9394 (m-80) cc_final: 0.9151 (m-80) REVERT: B 1584 MET cc_start: 0.9532 (mtt) cc_final: 0.9158 (mmp) REVERT: B 1703 LYS cc_start: 0.8874 (mttt) cc_final: 0.8532 (mttt) REVERT: B 1704 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7612 (mp0) REVERT: B 1741 LYS cc_start: 0.9621 (tppt) cc_final: 0.9413 (tppt) REVERT: B 1769 GLU cc_start: 0.8351 (mp0) cc_final: 0.7946 (mp0) REVERT: B 1852 VAL cc_start: 0.9780 (t) cc_final: 0.9565 (m) REVERT: B 1946 ASN cc_start: 0.9188 (t0) cc_final: 0.8985 (t0) REVERT: B 1955 LEU cc_start: 0.9113 (tt) cc_final: 0.8822 (pp) REVERT: B 1961 LYS cc_start: 0.9006 (mtmt) cc_final: 0.8516 (mmtt) REVERT: B 1996 MET cc_start: 0.8916 (mpp) cc_final: 0.8517 (pmm) REVERT: B 2040 PHE cc_start: 0.8062 (p90) cc_final: 0.7583 (p90) REVERT: B 2052 MET cc_start: 0.8944 (mmm) cc_final: 0.8572 (mmp) REVERT: B 2094 TRP cc_start: 0.8408 (m100) cc_final: 0.7709 (m100) REVERT: B 2100 LYS cc_start: 0.9423 (mttt) cc_final: 0.9174 (mmmt) REVERT: B 2179 MET cc_start: 0.9183 (tpp) cc_final: 0.8955 (tpp) REVERT: B 2206 LYS cc_start: 0.9390 (mttt) cc_final: 0.9048 (ptpp) REVERT: B 2338 LEU cc_start: 0.9571 (mt) cc_final: 0.9265 (mt) REVERT: B 2339 MET cc_start: 0.9353 (mmt) cc_final: 0.8768 (mmt) REVERT: B 2401 MET cc_start: 0.8582 (mmm) cc_final: 0.8381 (mmm) REVERT: B 2407 ARG cc_start: 0.9035 (mtt180) cc_final: 0.8650 (tpt170) REVERT: B 2438 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8638 (mt-10) REVERT: B 2505 PHE cc_start: 0.8915 (t80) cc_final: 0.8486 (t80) REVERT: B 2526 MET cc_start: 0.8496 (tpt) cc_final: 0.8117 (tpt) REVERT: B 2529 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7823 (mp0) REVERT: B 2548 GLU cc_start: 0.9410 (pm20) cc_final: 0.8899 (pp20) REVERT: B 2551 MET cc_start: 0.9397 (tpt) cc_final: 0.9172 (tpt) REVERT: B 2596 GLU cc_start: 0.8024 (pp20) cc_final: 0.7808 (pp20) REVERT: B 2608 ARG cc_start: 0.7679 (mtt90) cc_final: 0.6930 (ttm170) REVERT: B 2612 LEU cc_start: 0.9524 (mt) cc_final: 0.9315 (mt) REVERT: B 2633 LEU cc_start: 0.8947 (tt) cc_final: 0.8694 (mt) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.1882 time to fit residues: 145.3381 Evaluate side-chains 393 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 520 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 202 optimal weight: 8.9990 chunk 440 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 434 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 420 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1830 GLN A2015 ASN A2019 ASN ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2123 ASN A2144 GLN ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1667 GLN B1737 HIS ** B1917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1937 HIS B2019 ASN ** B2081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.076226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.055880 restraints weight = 180864.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057753 restraints weight = 111751.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059092 restraints weight = 78467.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.060059 restraints weight = 59973.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060750 restraints weight = 48824.552| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33739 Z= 0.138 Angle : 0.703 11.261 46280 Z= 0.377 Chirality : 0.043 0.241 5753 Planarity : 0.005 0.097 6264 Dihedral : 6.876 60.657 5588 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.53 % Favored : 86.00 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 2.58 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.12), residues: 5364 helix: 0.83 (0.09), residues: 3639 sheet: -3.02 (0.57), residues: 61 loop : -3.53 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B1904 TYR 0.035 0.002 TYR B2097 PHE 0.019 0.001 PHE A2009 TRP 0.054 0.003 TRP A2104 HIS 0.013 0.001 HIS B2129 Details of bonding type rmsd covalent geometry : bond 0.00273 (33737) covalent geometry : angle 0.70171 (46276) SS BOND : bond 0.00093 ( 2) SS BOND : angle 3.75413 ( 4) hydrogen bonds : bond 0.03561 ( 2089) hydrogen bonds : angle 5.00076 ( 6177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 1.264 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: A 1537 LEU cc_start: 0.9315 (mt) cc_final: 0.9111 (mt) REVERT: A 1582 PHE cc_start: 0.9187 (m-80) cc_final: 0.8702 (m-80) REVERT: A 1673 LEU cc_start: 0.9560 (mt) cc_final: 0.9285 (mt) REVERT: A 1683 MET cc_start: 0.8607 (mmm) cc_final: 0.8034 (mmm) REVERT: A 1699 GLU cc_start: 0.8770 (mp0) cc_final: 0.8405 (pm20) REVERT: A 1737 HIS cc_start: 0.8868 (t70) cc_final: 0.8182 (t70) REVERT: A 1743 MET cc_start: 0.9467 (mtm) cc_final: 0.9072 (ptp) REVERT: A 1946 ASN cc_start: 0.9572 (t0) cc_final: 0.9306 (t0) REVERT: A 2011 GLU cc_start: 0.8582 (pp20) cc_final: 0.8263 (tm-30) REVERT: A 2058 MET cc_start: 0.8188 (ptm) cc_final: 0.7296 (ppp) REVERT: A 2078 TYR cc_start: 0.8489 (t80) cc_final: 0.8147 (t80) REVERT: A 2082 PHE cc_start: 0.6926 (t80) cc_final: 0.6270 (t80) REVERT: A 2087 MET cc_start: 0.7631 (tpt) cc_final: 0.6907 (tpt) REVERT: A 2093 LEU cc_start: 0.9343 (mt) cc_final: 0.8623 (mt) REVERT: A 2097 TYR cc_start: 0.8309 (m-10) cc_final: 0.7988 (m-80) REVERT: A 2099 THR cc_start: 0.9232 (p) cc_final: 0.8917 (p) REVERT: A 2138 PHE cc_start: 0.9202 (m-80) cc_final: 0.8751 (m-80) REVERT: A 2140 THR cc_start: 0.8881 (t) cc_final: 0.8241 (t) REVERT: A 2155 GLU cc_start: 0.8980 (tp30) cc_final: 0.8361 (tp30) REVERT: A 2166 LYS cc_start: 0.9223 (mttt) cc_final: 0.9013 (ptmm) REVERT: A 2179 MET cc_start: 0.9377 (mmp) cc_final: 0.9124 (mmm) REVERT: A 2195 LYS cc_start: 0.9366 (mttt) cc_final: 0.9109 (tptp) REVERT: A 2339 MET cc_start: 0.9105 (mmt) cc_final: 0.8435 (mmt) REVERT: A 2429 LEU cc_start: 0.9529 (mt) cc_final: 0.9015 (tp) REVERT: A 2437 HIS cc_start: 0.9148 (t70) cc_final: 0.8927 (t70) REVERT: A 2458 CYS cc_start: 0.9648 (m) cc_final: 0.9268 (t) REVERT: A 2469 TYR cc_start: 0.9328 (t80) cc_final: 0.8970 (t80) REVERT: A 2505 PHE cc_start: 0.8693 (t80) cc_final: 0.7896 (t80) REVERT: A 2519 MET cc_start: 0.9233 (mtp) cc_final: 0.8975 (mtp) REVERT: A 2523 MET cc_start: 0.6905 (ptt) cc_final: 0.6617 (ptt) REVERT: A 2531 LEU cc_start: 0.9542 (mt) cc_final: 0.9264 (mt) REVERT: A 2534 ARG cc_start: 0.8986 (mmm-85) cc_final: 0.8403 (tpp-160) REVERT: A 2537 GLU cc_start: 0.9127 (pt0) cc_final: 0.8589 (pt0) REVERT: A 2543 MET cc_start: 0.9390 (mmp) cc_final: 0.9179 (ttp) REVERT: A 2617 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8370 (tm-30) REVERT: A 2636 MET cc_start: 0.8843 (mmp) cc_final: 0.8487 (mmm) REVERT: B 1553 MET cc_start: 0.8645 (mpp) cc_final: 0.8424 (mpp) REVERT: B 1575 GLN cc_start: 0.8890 (mt0) cc_final: 0.8516 (mp10) REVERT: B 1582 PHE cc_start: 0.9383 (m-80) cc_final: 0.9157 (m-80) REVERT: B 1584 MET cc_start: 0.9516 (mtt) cc_final: 0.9197 (mmp) REVERT: B 1651 TYR cc_start: 0.8354 (m-80) cc_final: 0.7946 (m-80) REVERT: B 1703 LYS cc_start: 0.8721 (mttt) cc_final: 0.8463 (mttt) REVERT: B 1895 ARG cc_start: 0.9250 (mpp80) cc_final: 0.9004 (mtm-85) REVERT: B 1932 ARG cc_start: 0.9416 (tmm160) cc_final: 0.8663 (ttp80) REVERT: B 1961 LYS cc_start: 0.8886 (mtmt) cc_final: 0.8427 (mmtt) REVERT: B 1964 TRP cc_start: 0.8389 (t60) cc_final: 0.8113 (t60) REVERT: B 1996 MET cc_start: 0.8854 (mpp) cc_final: 0.8460 (pmm) REVERT: B 2003 MET cc_start: 0.8747 (tpt) cc_final: 0.8535 (tpt) REVERT: B 2040 PHE cc_start: 0.8034 (p90) cc_final: 0.7688 (p90) REVERT: B 2052 MET cc_start: 0.8910 (mmm) cc_final: 0.8544 (mmp) REVERT: B 2055 ASP cc_start: 0.9667 (m-30) cc_final: 0.9448 (m-30) REVERT: B 2070 LEU cc_start: 0.9052 (mm) cc_final: 0.8789 (mm) REVERT: B 2072 PHE cc_start: 0.8786 (m-80) cc_final: 0.8430 (m-80) REVERT: B 2094 TRP cc_start: 0.8321 (m100) cc_final: 0.7594 (m100) REVERT: B 2179 MET cc_start: 0.9289 (tpp) cc_final: 0.9052 (tpp) REVERT: B 2206 LYS cc_start: 0.9406 (mttt) cc_final: 0.9026 (ptpp) REVERT: B 2339 MET cc_start: 0.9311 (mmt) cc_final: 0.8557 (mmt) REVERT: B 2401 MET cc_start: 0.8473 (mmm) cc_final: 0.8206 (mmm) REVERT: B 2438 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8591 (mt-10) REVERT: B 2464 MET cc_start: 0.9212 (tpt) cc_final: 0.8325 (tpp) REVERT: B 2473 LEU cc_start: 0.8784 (pt) cc_final: 0.8309 (mt) REVERT: B 2505 PHE cc_start: 0.8949 (t80) cc_final: 0.8601 (t80) REVERT: B 2529 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7823 (mp0) REVERT: B 2633 LEU cc_start: 0.8834 (tt) cc_final: 0.8579 (mt) outliers start: 0 outliers final: 0 residues processed: 479 average time/residue: 0.1920 time to fit residues: 151.9991 Evaluate side-chains 418 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 5 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 50 optimal weight: 40.0000 chunk 239 optimal weight: 6.9990 chunk 497 optimal weight: 1.9990 chunk 117 optimal weight: 30.0000 chunk 189 optimal weight: 2.9990 chunk 521 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 chunk 270 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1748 GLN ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2123 ASN A2144 GLN ** A2151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1737 HIS ** B1917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1937 HIS ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS ** B2480 ASN ** 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 = 0.3522 r_free = 0.3522 target = 0.073317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.053331 restraints weight = 190215.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.055087 restraints weight = 118422.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.056341 restraints weight = 83530.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.057271 restraints weight = 64123.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057911 restraints weight = 52406.326| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 33739 Z= 0.236 Angle : 0.770 10.131 46280 Z= 0.421 Chirality : 0.045 0.233 5753 Planarity : 0.005 0.098 6264 Dihedral : 6.941 61.047 5588 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.97 % Favored : 84.55 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.12), residues: 5364 helix: 0.80 (0.09), residues: 3656 sheet: -2.27 (0.60), residues: 69 loop : -3.65 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2089 TYR 0.052 0.003 TYR B1848 PHE 0.025 0.002 PHE B2557 TRP 0.057 0.003 TRP A2104 HIS 0.009 0.002 HIS B2492 Details of bonding type rmsd covalent geometry : bond 0.00454 (33737) covalent geometry : angle 0.76989 (46276) SS BOND : bond 0.00243 ( 2) SS BOND : angle 3.23245 ( 4) hydrogen bonds : bond 0.03997 ( 2089) hydrogen bonds : angle 5.12680 ( 6177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 1.217 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: A 1582 PHE cc_start: 0.9245 (m-80) cc_final: 0.8768 (m-80) REVERT: A 1584 MET cc_start: 0.8933 (mpp) cc_final: 0.8545 (mpp) REVERT: A 1673 LEU cc_start: 0.9532 (mt) cc_final: 0.9251 (mt) REVERT: A 1683 MET cc_start: 0.8698 (mmm) cc_final: 0.8002 (mmm) REVERT: A 1699 GLU cc_start: 0.8989 (mp0) cc_final: 0.8620 (pm20) REVERT: A 1737 HIS cc_start: 0.8956 (t70) cc_final: 0.8200 (t70) REVERT: A 2040 PHE cc_start: 0.8364 (p90) cc_final: 0.8163 (p90) REVERT: A 2058 MET cc_start: 0.8223 (ptm) cc_final: 0.7326 (ppp) REVERT: A 2078 TYR cc_start: 0.8629 (t80) cc_final: 0.8245 (t80) REVERT: A 2082 PHE cc_start: 0.7305 (t80) cc_final: 0.6608 (t80) REVERT: A 2090 MET cc_start: 0.9106 (tpt) cc_final: 0.8442 (tpp) REVERT: A 2093 LEU cc_start: 0.9370 (mt) cc_final: 0.8623 (mt) REVERT: A 2097 TYR cc_start: 0.8365 (m-10) cc_final: 0.8066 (m-80) REVERT: A 2138 PHE cc_start: 0.9255 (m-80) cc_final: 0.8907 (m-80) REVERT: A 2140 THR cc_start: 0.8951 (t) cc_final: 0.8302 (t) REVERT: A 2144 GLN cc_start: 0.9331 (mm-40) cc_final: 0.8884 (mm110) REVERT: A 2155 GLU cc_start: 0.9034 (tp30) cc_final: 0.8433 (tp30) REVERT: A 2179 MET cc_start: 0.9398 (mmp) cc_final: 0.9122 (mmm) REVERT: A 2339 MET cc_start: 0.9173 (mmt) cc_final: 0.8548 (mmt) REVERT: A 2429 LEU cc_start: 0.9575 (mt) cc_final: 0.9058 (tp) REVERT: A 2437 HIS cc_start: 0.9245 (t70) cc_final: 0.8926 (t70) REVERT: A 2458 CYS cc_start: 0.9660 (m) cc_final: 0.9360 (t) REVERT: A 2464 MET cc_start: 0.9527 (ttt) cc_final: 0.9228 (ttp) REVERT: A 2531 LEU cc_start: 0.9567 (mt) cc_final: 0.9248 (mt) REVERT: A 2537 GLU cc_start: 0.9193 (pt0) cc_final: 0.8841 (pt0) REVERT: A 2600 GLN cc_start: 0.9579 (mt0) cc_final: 0.9259 (tp-100) REVERT: A 2612 LEU cc_start: 0.9294 (tp) cc_final: 0.9083 (tp) REVERT: A 2617 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8221 (tm-30) REVERT: A 2636 MET cc_start: 0.8952 (mmp) cc_final: 0.8650 (mmm) REVERT: B 1553 MET cc_start: 0.8605 (mpp) cc_final: 0.8262 (mpp) REVERT: B 1575 GLN cc_start: 0.8931 (mt0) cc_final: 0.8474 (mp10) REVERT: B 1582 PHE cc_start: 0.9404 (m-80) cc_final: 0.9171 (m-80) REVERT: B 1584 MET cc_start: 0.9497 (mtt) cc_final: 0.9156 (mmp) REVERT: B 1703 LYS cc_start: 0.8989 (mttt) cc_final: 0.8684 (mttt) REVERT: B 1741 LYS cc_start: 0.9603 (tppt) cc_final: 0.9342 (tppt) REVERT: B 1776 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8862 (mt-10) REVERT: B 1932 ARG cc_start: 0.9474 (tmm160) cc_final: 0.9101 (ttp80) REVERT: B 1946 ASN cc_start: 0.9111 (t0) cc_final: 0.8869 (t0) REVERT: B 1961 LYS cc_start: 0.8937 (mtmt) cc_final: 0.8493 (mmtt) REVERT: B 1964 TRP cc_start: 0.8427 (t60) cc_final: 0.8082 (t60) REVERT: B 1996 MET cc_start: 0.8917 (mpp) cc_final: 0.8565 (pmm) REVERT: B 2003 MET cc_start: 0.8755 (tpt) cc_final: 0.7530 (tpp) REVERT: B 2040 PHE cc_start: 0.8163 (p90) cc_final: 0.7635 (p90) REVERT: B 2052 MET cc_start: 0.8954 (mmm) cc_final: 0.8526 (mmp) REVERT: B 2055 ASP cc_start: 0.9690 (m-30) cc_final: 0.9467 (m-30) REVERT: B 2058 MET cc_start: 0.8941 (ttp) cc_final: 0.8254 (ppp) REVERT: B 2094 TRP cc_start: 0.8452 (m100) cc_final: 0.7588 (m100) REVERT: B 2097 TYR cc_start: 0.7334 (m-80) cc_final: 0.6849 (m-80) REVERT: B 2151 HIS cc_start: 0.6057 (m-70) cc_final: 0.5672 (m-70) REVERT: B 2179 MET cc_start: 0.9243 (tpp) cc_final: 0.9041 (tpp) REVERT: B 2206 LYS cc_start: 0.9382 (mttt) cc_final: 0.9092 (ptpp) REVERT: B 2324 MET cc_start: 0.9134 (mmp) cc_final: 0.8814 (mmm) REVERT: B 2336 CYS cc_start: 0.9653 (t) cc_final: 0.9449 (m) REVERT: B 2339 MET cc_start: 0.9321 (mmt) cc_final: 0.8694 (mmt) REVERT: B 2438 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8630 (mt-10) REVERT: B 2464 MET cc_start: 0.9275 (tpt) cc_final: 0.8956 (tpt) REVERT: B 2505 PHE cc_start: 0.9002 (t80) cc_final: 0.8602 (t80) REVERT: B 2526 MET cc_start: 0.8322 (tpp) cc_final: 0.7952 (tpp) REVERT: B 2529 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7921 (mp0) REVERT: B 2596 GLU cc_start: 0.8340 (pp20) cc_final: 0.8105 (pp20) REVERT: B 2622 TYR cc_start: 0.8746 (t80) cc_final: 0.8506 (t80) REVERT: B 2633 LEU cc_start: 0.8976 (tt) cc_final: 0.8697 (mt) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.1747 time to fit residues: 131.5006 Evaluate side-chains 387 residues out of total 4814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 231 optimal weight: 1.9990 chunk 338 optimal weight: 0.9990 chunk 362 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 353 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 373 optimal weight: 0.0980 chunk 413 optimal weight: 0.7980 chunk 126 optimal weight: 30.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1748 GLN ** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2015 ASN ** A2056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2085 GLN A2123 ASN ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1737 HIS ** B1917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1937 HIS ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2518 ASN B2597 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.076823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056205 restraints weight = 182586.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.058139 restraints weight = 113054.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059486 restraints weight = 79046.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.060486 restraints weight = 60408.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.061189 restraints weight = 48999.493| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 33739 Z= 0.133 Angle : 0.720 10.962 46280 Z= 0.383 Chirality : 0.044 0.305 5753 Planarity : 0.004 0.097 6264 Dihedral : 6.662 59.855 5588 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.86 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 2.58 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.13), residues: 5364 helix: 1.11 (0.09), residues: 3662 sheet: -2.08 (0.59), residues: 71 loop : -3.53 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2089 TYR 0.031 0.002 TYR B2097 PHE 0.038 0.002 PHE B2157 TRP 0.055 0.002 TRP A2104 HIS 0.007 0.001 HIS B2492 Details of bonding type rmsd covalent geometry : bond 0.00270 (33737) covalent geometry : angle 0.71985 (46276) SS BOND : bond 0.00043 ( 2) SS BOND : angle 3.23180 ( 4) hydrogen bonds : bond 0.03521 ( 2089) hydrogen bonds : angle 4.82902 ( 6177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5443.78 seconds wall clock time: 94 minutes 32.95 seconds (5672.95 seconds total)