Starting phenix.real_space_refine on Fri Sep 19 05:12:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i26_0328/09_2025/6i26_0328_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i26_0328/09_2025/6i26_0328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6i26_0328/09_2025/6i26_0328_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i26_0328/09_2025/6i26_0328_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i26_0328/09_2025/6i26_0328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i26_0328/09_2025/6i26_0328.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 32 5.16 5 C 14329 2.51 5 N 4101 2.21 5 O 4303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22765 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3150, 19447 Classifications: {'peptide': 3150} Incomplete info: {'truncation_to_alanine': 1795} Link IDs: {'CIS': 1, 'PTRANS': 104, 'TRANS': 3044} Chain breaks: 25 Unresolved chain link angles: 67 Unresolved non-hydrogen bonds: 5919 Unresolved non-hydrogen angles: 7616 Unresolved non-hydrogen dihedrals: 4720 Unresolved non-hydrogen chiralities: 549 Planarities with less than four sites: {'UNK:plan-1': 190, 'GLU:plan': 146, 'PHE:plan': 81, 'TYR:plan': 31, 'GLN:plan1': 56, 'ASP:plan': 110, 'HIS:plan': 32, 'ARG:plan': 78, 'ASN:plan1': 102, 'TRP:plan': 16} Unresolved non-hydrogen planarities: 3031 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 7, 'TRANS': 429} Chain breaks: 9 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'UNK:plan-1': 31, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 9, 'ASP:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 5.19, per 1000 atoms: 0.23 Number of scatterers: 22765 At special positions: 0 Unit cell: (135.16, 147.15, 284.49, 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 32 16.00 O 4303 8.00 N 4101 7.00 C 14329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 898.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6910 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 11 sheets defined 57.7% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.608A pdb=" N UNK A 26 " --> pdb=" O UNK A 22 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N UNK A 30 " --> pdb=" O UNK A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.748A pdb=" N UNK A 77 " --> pdb=" O UNK A 73 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N UNK A 78 " --> pdb=" O UNK A 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N UNK A 79 " --> pdb=" O UNK A 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N UNK A 82 " --> pdb=" O UNK A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.797A pdb=" N UNK A 90 " --> pdb=" O UNK A 86 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N UNK A 93 " --> pdb=" O UNK A 89 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N UNK A 94 " --> pdb=" O UNK A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.598A pdb=" N UNK A 118 " --> pdb=" O UNK A 115 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N UNK A 119 " --> pdb=" O UNK A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.594A pdb=" N UNK A 127 " --> pdb=" O UNK A 123 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N UNK A 130 " --> pdb=" O UNK A 126 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK A 132 " --> pdb=" O UNK A 128 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N UNK A 138 " --> pdb=" O UNK A 134 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N UNK A 139 " --> pdb=" O UNK A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.033A pdb=" N UNK A 160 " --> pdb=" O UNK A 156 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N UNK A 161 " --> pdb=" O UNK A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 170 removed outlier: 4.018A pdb=" N UNK A 170 " --> pdb=" O UNK A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.583A pdb=" N UNK A 177 " --> pdb=" O UNK A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 removed outlier: 4.039A pdb=" N UNK A 190 " --> pdb=" O UNK A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 238 through 250 removed outlier: 3.581A pdb=" N GLU A 242 " --> pdb=" O PRO A 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.798A pdb=" N ASP A 280 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.611A pdb=" N LYS A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 332 removed outlier: 3.661A pdb=" N ILE A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 removed outlier: 3.703A pdb=" N ALA A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 402 removed outlier: 4.240A pdb=" N ILE A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.865A pdb=" N LEU A 407 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.911A pdb=" N HIS A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 472 " --> pdb=" O HIS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 492 removed outlier: 3.600A pdb=" N ILE A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP A 486 " --> pdb=" O PRO A 482 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 512 through 521 removed outlier: 3.899A pdb=" N ASP A 516 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 removed outlier: 3.777A pdb=" N ILE A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 548 removed outlier: 4.649A pdb=" N ASP A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.551A pdb=" N ILE A 570 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN A 571 " --> pdb=" O PRO A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'A' and resid 631 through 645 removed outlier: 4.105A pdb=" N LEU A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 642 " --> pdb=" O GLN A 638 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 643 " --> pdb=" O ILE A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 666 removed outlier: 3.822A pdb=" N VAL A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 666 " --> pdb=" O VAL A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 710 removed outlier: 3.626A pdb=" N ILE A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 removed outlier: 3.868A pdb=" N ASN A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 749 removed outlier: 3.802A pdb=" N VAL A 740 " --> pdb=" O GLN A 736 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 741 " --> pdb=" O TRP A 737 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 796 removed outlier: 3.750A pdb=" N PHE A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 removed outlier: 4.207A pdb=" N LYS A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR A 819 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 844 removed outlier: 4.265A pdb=" N SER A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 894 removed outlier: 3.743A pdb=" N MET A 890 " --> pdb=" O ARG A 886 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG A 893 " --> pdb=" O PRO A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 929 through 938 removed outlier: 3.867A pdb=" N LEU A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.539A pdb=" N LEU A 964 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 Processing helix chain 'A' and resid 974 through 979 Processing helix chain 'A' and resid 997 through 1004 removed outlier: 3.914A pdb=" N GLU A1001 " --> pdb=" O ASP A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1072 removed outlier: 3.755A pdb=" N LYS A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN A1064 " --> pdb=" O PHE A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.650A pdb=" N MET A1092 " --> pdb=" O GLY A1088 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP A1098 " --> pdb=" O LYS A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1141 Processing helix chain 'A' and resid 1224 through 1233 removed outlier: 3.846A pdb=" N GLU A1228 " --> pdb=" O GLN A1224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A1229 " --> pdb=" O ASP A1225 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A1232 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A1233 " --> pdb=" O ILE A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1241 removed outlier: 3.542A pdb=" N SER A1240 " --> pdb=" O GLN A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.576A pdb=" N VAL A1246 " --> pdb=" O LYS A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1277 removed outlier: 3.536A pdb=" N TRP A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1297 removed outlier: 3.626A pdb=" N LEU A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A1289 " --> pdb=" O TYR A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1318 removed outlier: 4.174A pdb=" N VAL A1316 " --> pdb=" O THR A1312 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1359 removed outlier: 3.780A pdb=" N ARG A1348 " --> pdb=" O THR A1344 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A1349 " --> pdb=" O LYS A1345 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A1352 " --> pdb=" O ARG A1348 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A1357 " --> pdb=" O LEU A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1385 removed outlier: 3.622A pdb=" N GLN A1379 " --> pdb=" O THR A1375 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A1382 " --> pdb=" O CYS A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1405 removed outlier: 4.011A pdb=" N LEU A1404 " --> pdb=" O THR A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1485 removed outlier: 3.822A pdb=" N GLN A1481 " --> pdb=" O GLY A1477 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A1482 " --> pdb=" O PRO A1478 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A1483 " --> pdb=" O LEU A1479 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A1484 " --> pdb=" O ILE A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1505 removed outlier: 3.542A pdb=" N LEU A1502 " --> pdb=" O ASP A1498 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A1505 " --> pdb=" O VAL A1501 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1550 removed outlier: 4.237A pdb=" N LEU A1550 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1578 removed outlier: 4.155A pdb=" N ILE A1575 " --> pdb=" O ASP A1571 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A1576 " --> pdb=" O VAL A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1600 Proline residue: A1590 - end of helix removed outlier: 3.660A pdb=" N GLU A1596 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A1599 " --> pdb=" O SER A1595 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1622 removed outlier: 3.586A pdb=" N VAL A1611 " --> pdb=" O ALA A1607 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A1617 " --> pdb=" O SER A1613 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A1622 " --> pdb=" O LEU A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1635 Processing helix chain 'A' and resid 1636 through 1641 removed outlier: 3.745A pdb=" N GLN A1640 " --> pdb=" O THR A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1646 removed outlier: 4.299A pdb=" N VAL A1645 " --> pdb=" O ALA A1642 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A1646 " --> pdb=" O SER A1643 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1642 through 1646' Processing helix chain 'A' and resid 1652 through 1668 removed outlier: 3.556A pdb=" N LEU A1665 " --> pdb=" O ASN A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1724 through 1735 removed outlier: 3.549A pdb=" N SER A1728 " --> pdb=" O PRO A1724 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A1730 " --> pdb=" O THR A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1736 through 1738 No H-bonds generated for 'chain 'A' and resid 1736 through 1738' Processing helix chain 'A' and resid 1752 through 1764 removed outlier: 3.550A pdb=" N ALA A1759 " --> pdb=" O SER A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1831 Processing helix chain 'A' and resid 1872 through 1877 removed outlier: 3.884A pdb=" N VAL A1876 " --> pdb=" O PRO A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1888 through 1896 removed outlier: 3.908A pdb=" N LEU A1893 " --> pdb=" O SER A1889 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1894 " --> pdb=" O ASP A1890 " (cutoff:3.500A) Processing helix chain 'A' and resid 1906 through 1925 removed outlier: 3.537A pdb=" N MET A1911 " --> pdb=" O ILE A1907 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A1912 " --> pdb=" O ILE A1908 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A1917 " --> pdb=" O LYS A1913 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A1921 " --> pdb=" O THR A1917 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A1925 " --> pdb=" O GLN A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1950 removed outlier: 3.820A pdb=" N THR A1942 " --> pdb=" O ASN A1938 " (cutoff:3.500A) Processing helix chain 'A' and resid 1961 through 1966 removed outlier: 4.186A pdb=" N ASP A1965 " --> pdb=" O ASP A1962 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A1966 " --> pdb=" O PHE A1963 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1978 Processing helix chain 'A' and resid 1979 through 1989 removed outlier: 3.726A pdb=" N LEU A1983 " --> pdb=" O ASN A1979 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A1988 " --> pdb=" O LEU A1984 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A1989 " --> pdb=" O ILE A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2046 removed outlier: 3.705A pdb=" N SER A2039 " --> pdb=" O ALA A2035 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A2041 " --> pdb=" O TYR A2037 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A2044 " --> pdb=" O VAL A2040 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN A2045 " --> pdb=" O LEU A2041 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN A2046 " --> pdb=" O LYS A2042 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2071 removed outlier: 3.577A pdb=" N LEU A2067 " --> pdb=" O THR A2063 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A2070 " --> pdb=" O PHE A2066 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A2071 " --> pdb=" O LEU A2067 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2089 removed outlier: 3.660A pdb=" N ILE A2089 " --> pdb=" O ASP A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2098 through 2120 removed outlier: 3.895A pdb=" N TYR A2104 " --> pdb=" O ARG A2100 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A2105 " --> pdb=" O GLN A2101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A2115 " --> pdb=" O ASN A2111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A2119 " --> pdb=" O GLU A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2126 through 2143 removed outlier: 4.337A pdb=" N GLU A2132 " --> pdb=" O THR A2128 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A2136 " --> pdb=" O GLU A2132 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A2137 " --> pdb=" O GLY A2133 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A2142 " --> pdb=" O LYS A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2149 through 2160 removed outlier: 3.534A pdb=" N ARG A2154 " --> pdb=" O PHE A2150 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2184 removed outlier: 3.968A pdb=" N LEU A2170 " --> pdb=" O GLY A2166 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A2173 " --> pdb=" O LEU A2169 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A2174 " --> pdb=" O LEU A2170 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A2180 " --> pdb=" O ASN A2176 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A2183 " --> pdb=" O LYS A2179 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A2184 " --> pdb=" O MET A2180 " (cutoff:3.500A) Processing helix chain 'A' and resid 2185 through 2187 No H-bonds generated for 'chain 'A' and resid 2185 through 2187' Processing helix chain 'A' and resid 2197 through 2206 removed outlier: 3.575A pdb=" N LYS A2201 " --> pdb=" O GLY A2197 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A2204 " --> pdb=" O VAL A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2221 through 2227 removed outlier: 3.569A pdb=" N LEU A2225 " --> pdb=" O LEU A2222 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A2226 " --> pdb=" O ASP A2223 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A2227 " --> pdb=" O ARG A2224 " (cutoff:3.500A) Processing helix chain 'A' and resid 2284 through 2289 Processing helix chain 'A' and resid 2337 through 2352 removed outlier: 3.975A pdb=" N PHE A2342 " --> pdb=" O ARG A2338 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A2344 " --> pdb=" O CYS A2340 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A2345 " --> pdb=" O ILE A2341 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A2346 " --> pdb=" O PHE A2342 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A2348 " --> pdb=" O GLN A2344 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A2349 " --> pdb=" O VAL A2345 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2383 removed outlier: 4.034A pdb=" N GLY A2374 " --> pdb=" O LEU A2370 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A2375 " --> pdb=" O GLY A2371 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A2378 " --> pdb=" O GLY A2374 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N CYS A2383 " --> pdb=" O ASN A2379 " (cutoff:3.500A) Processing helix chain 'A' and resid 2389 through 2403 removed outlier: 3.735A pdb=" N TYR A2396 " --> pdb=" O ALA A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2415 removed outlier: 3.583A pdb=" N TYR A2415 " --> pdb=" O ILE A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2415 through 2426 removed outlier: 3.770A pdb=" N LEU A2420 " --> pdb=" O LYS A2416 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A2421 " --> pdb=" O PRO A2417 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A2424 " --> pdb=" O LEU A2420 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A2426 " --> pdb=" O PHE A2422 " (cutoff:3.500A) Processing helix chain 'A' and resid 2445 through 2451 removed outlier: 3.706A pdb=" N THR A2449 " --> pdb=" O TYR A2445 " (cutoff:3.500A) Processing helix chain 'A' and resid 2460 through 2488 removed outlier: 4.000A pdb=" N TYR A2464 " --> pdb=" O PRO A2460 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A2465 " --> pdb=" O GLU A2461 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU A2466 " --> pdb=" O SER A2462 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A2469 " --> pdb=" O LEU A2465 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A2470 " --> pdb=" O LEU A2466 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A2471 " --> pdb=" O SER A2467 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A2473 " --> pdb=" O LEU A2469 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA A2478 " --> pdb=" O ASN A2474 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A2481 " --> pdb=" O ASN A2477 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A2482 " --> pdb=" O ALA A2478 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A2487 " --> pdb=" O ASN A2483 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A2488 " --> pdb=" O GLU A2484 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2503 removed outlier: 3.713A pdb=" N SER A2500 " --> pdb=" O TYR A2496 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A2503 " --> pdb=" O LEU A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2522 through 2532 removed outlier: 3.589A pdb=" N VAL A2527 " --> pdb=" O ASN A2523 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A2532 " --> pdb=" O MET A2528 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2547 Processing helix chain 'A' and resid 2549 through 2560 removed outlier: 3.508A pdb=" N ILE A2553 " --> pdb=" O ASP A2549 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A2555 " --> pdb=" O LEU A2551 " (cutoff:3.500A) Processing helix chain 'A' and resid 2565 through 2570 Processing helix chain 'A' and resid 2571 through 2576 removed outlier: 3.740A pdb=" N ILE A2576 " --> pdb=" O TYR A2572 " (cutoff:3.500A) Processing helix chain 'A' and resid 2577 through 2584 Processing helix chain 'A' and resid 2590 through 2595 removed outlier: 4.342A pdb=" N PHE A2594 " --> pdb=" O GLU A2590 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A2595 " --> pdb=" O ILE A2591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2590 through 2595' Processing helix chain 'A' and resid 2600 through 2606 removed outlier: 3.656A pdb=" N VAL A2604 " --> pdb=" O GLU A2600 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A2606 " --> pdb=" O THR A2602 " (cutoff:3.500A) Processing helix chain 'A' and resid 2612 through 2617 Processing helix chain 'A' and resid 2627 through 2649 removed outlier: 3.875A pdb=" N TRP A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A2632 " --> pdb=" O SER A2628 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A2633 " --> pdb=" O ASN A2629 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A2636 " --> pdb=" O LEU A2632 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A2638 " --> pdb=" O PHE A2634 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A2643 " --> pdb=" O ASN A2639 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP A2645 " --> pdb=" O SER A2641 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A2646 " --> pdb=" O GLU A2642 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A2647 " --> pdb=" O LYS A2643 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A2649 " --> pdb=" O ASP A2645 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2674 removed outlier: 3.923A pdb=" N ASP A2664 " --> pdb=" O LYS A2660 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A2666 " --> pdb=" O LEU A2662 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG A2667 " --> pdb=" O MET A2663 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A2674 " --> pdb=" O ASN A2670 " (cutoff:3.500A) Processing helix chain 'A' and resid 2680 through 2700 removed outlier: 3.649A pdb=" N SER A2686 " --> pdb=" O ASN A2682 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A2687 " --> pdb=" O LEU A2683 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A2688 " --> pdb=" O LEU A2684 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A2699 " --> pdb=" O LEU A2695 " (cutoff:3.500A) Processing helix chain 'A' and resid 2710 through 2720 removed outlier: 3.521A pdb=" N PHE A2714 " --> pdb=" O PHE A2710 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A2715 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A2718 " --> pdb=" O PHE A2714 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A2719 " --> pdb=" O ASP A2715 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR A2720 " --> pdb=" O ASN A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2726 through 2733 removed outlier: 3.893A pdb=" N ILE A2730 " --> pdb=" O THR A2726 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A2731 " --> pdb=" O ALA A2727 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A2732 " --> pdb=" O GLU A2728 " (cutoff:3.500A) Processing helix chain 'A' and resid 2740 through 2745 removed outlier: 3.540A pdb=" N LEU A2744 " --> pdb=" O ALA A2740 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A2745 " --> pdb=" O THR A2741 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2740 through 2745' Processing helix chain 'A' and resid 2757 through 2762 removed outlier: 4.691A pdb=" N TRP A2762 " --> pdb=" O PHE A2758 " (cutoff:3.500A) Processing helix chain 'A' and resid 2779 through 2791 removed outlier: 3.604A pdb=" N ASP A2784 " --> pdb=" O GLN A2780 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A2786 " --> pdb=" O LEU A2782 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A2787 " --> pdb=" O GLU A2783 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A2791 " --> pdb=" O ARG A2787 " (cutoff:3.500A) Processing helix chain 'A' and resid 2806 through 2815 Processing helix chain 'A' and resid 2817 through 2823 removed outlier: 3.540A pdb=" N LEU A2822 " --> pdb=" O SER A2818 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A2823 " --> pdb=" O PRO A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2830 through 2838 removed outlier: 4.012A pdb=" N TRP A2836 " --> pdb=" O MET A2832 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A2838 " --> pdb=" O LEU A2834 " (cutoff:3.500A) Processing helix chain 'A' and resid 2839 through 2845 Processing helix chain 'A' and resid 2853 through 2860 removed outlier: 3.592A pdb=" N LEU A2857 " --> pdb=" O THR A2853 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS A2858 " --> pdb=" O LEU A2854 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A2860 " --> pdb=" O GLU A2856 " (cutoff:3.500A) Processing helix chain 'A' and resid 2860 through 2865 Processing helix chain 'A' and resid 2868 through 2874 removed outlier: 3.901A pdb=" N THR A2872 " --> pdb=" O GLU A2868 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A2874 " --> pdb=" O ARG A2870 " (cutoff:3.500A) Processing helix chain 'A' and resid 2878 through 2886 removed outlier: 4.051A pdb=" N ALA A2884 " --> pdb=" O ALA A2880 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A2885 " --> pdb=" O LEU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2889 through 2904 removed outlier: 3.554A pdb=" N LEU A2893 " --> pdb=" O SER A2889 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A2896 " --> pdb=" O GLU A2892 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A2898 " --> pdb=" O GLY A2894 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A2900 " --> pdb=" O ALA A2896 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A2904 " --> pdb=" O PHE A2900 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2923 removed outlier: 3.894A pdb=" N TYR A2921 " --> pdb=" O ALA A2917 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A2923 " --> pdb=" O HIS A2919 " (cutoff:3.500A) Processing helix chain 'A' and resid 2924 through 2943 removed outlier: 3.664A pdb=" N SER A2934 " --> pdb=" O THR A2930 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A2941 " --> pdb=" O LEU A2937 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A2943 " --> pdb=" O LYS A2939 " (cutoff:3.500A) Processing helix chain 'A' and resid 2944 through 2947 Processing helix chain 'A' and resid 2954 through 2960 removed outlier: 3.909A pdb=" N LYS A2958 " --> pdb=" O ILE A2954 " (cutoff:3.500A) Processing helix chain 'A' and resid 2983 through 2992 removed outlier: 3.583A pdb=" N GLU A2987 " --> pdb=" O SER A2983 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A2989 " --> pdb=" O PHE A2985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2997 through 3009 removed outlier: 3.506A pdb=" N LYS A3002 " --> pdb=" O SER A2998 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU A3003 " --> pdb=" O ARG A2999 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A3004 " --> pdb=" O GLN A3000 " (cutoff:3.500A) Processing helix chain 'A' and resid 3014 through 3033 removed outlier: 4.174A pdb=" N ARG A3018 " --> pdb=" O GLN A3014 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A3019 " --> pdb=" O SER A3015 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU A3020 " --> pdb=" O ASP A3016 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET A3021 " --> pdb=" O ARG A3017 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A3027 " --> pdb=" O GLN A3023 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3069 removed outlier: 3.699A pdb=" N ILE A3046 " --> pdb=" O ASP A3042 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A3047 " --> pdb=" O LEU A3043 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A3050 " --> pdb=" O ILE A3046 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A3053 " --> pdb=" O GLY A3049 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A3054 " --> pdb=" O TYR A3050 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A3058 " --> pdb=" O ILE A3054 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU A3061 " --> pdb=" O GLY A3057 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A3063 " --> pdb=" O ASP A3059 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN A3064 " --> pdb=" O LEU A3060 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS A3067 " --> pdb=" O LEU A3063 " (cutoff:3.500A) Processing helix chain 'A' and resid 3087 through 3094 removed outlier: 3.815A pdb=" N LEU A3092 " --> pdb=" O ALA A3088 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3103 removed outlier: 3.677A pdb=" N LYS A3103 " --> pdb=" O SER A3099 " (cutoff:3.500A) Processing helix chain 'A' and resid 3111 through 3114 Processing helix chain 'A' and resid 3115 through 3124 removed outlier: 3.620A pdb=" N LEU A3120 " --> pdb=" O LEU A3116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A3121 " --> pdb=" O MET A3117 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A3124 " --> pdb=" O LEU A3120 " (cutoff:3.500A) Processing helix chain 'A' and resid 3133 through 3146 removed outlier: 4.313A pdb=" N ALA A3139 " --> pdb=" O ILE A3135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A3140 " --> pdb=" O PHE A3136 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A3142 " --> pdb=" O ALA A3138 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A3143 " --> pdb=" O ALA A3139 " (cutoff:3.500A) Processing helix chain 'A' and resid 3149 through 3155 Processing helix chain 'A' and resid 3203 through 3207 removed outlier: 3.650A pdb=" N TYR A3207 " --> pdb=" O LEU A3203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3203 through 3207' Processing helix chain 'A' and resid 3211 through 3218 removed outlier: 4.339A pdb=" N PHE A3218 " --> pdb=" O TYR A3214 " (cutoff:3.500A) Processing helix chain 'A' and resid 3232 through 3241 removed outlier: 4.042A pdb=" N ILE A3236 " --> pdb=" O SER A3232 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A3237 " --> pdb=" O GLY A3233 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR A3238 " --> pdb=" O ALA A3234 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A3239 " --> pdb=" O ILE A3235 " (cutoff:3.500A) Processing helix chain 'A' and resid 3253 through 3269 removed outlier: 3.540A pdb=" N LEU A3257 " --> pdb=" O LYS A3253 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A3258 " --> pdb=" O SER A3254 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A3259 " --> pdb=" O GLY A3255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A3260 " --> pdb=" O SER A3256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A3261 " --> pdb=" O LEU A3257 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN A3262 " --> pdb=" O SER A3258 " (cutoff:3.500A) Processing helix chain 'A' and resid 3287 through 3308 removed outlier: 4.317A pdb=" N LYS A3293 " --> pdb=" O PRO A3289 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A3299 " --> pdb=" O GLY A3295 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A3301 " --> pdb=" O ILE A3297 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A3304 " --> pdb=" O THR A3300 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A3306 " --> pdb=" O LEU A3302 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A3308 " --> pdb=" O SER A3304 " (cutoff:3.500A) Processing helix chain 'A' and resid 3316 through 3329 removed outlier: 3.876A pdb=" N TYR A3322 " --> pdb=" O LEU A3318 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A3329 " --> pdb=" O SER A3325 " (cutoff:3.500A) Processing helix chain 'A' and resid 3336 through 3358 removed outlier: 3.600A pdb=" N GLN A3340 " --> pdb=" O PRO A3336 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A3347 " --> pdb=" O LYS A3343 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A3348 " --> pdb=" O ILE A3344 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A3349 " --> pdb=" O GLU A3345 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A3356 " --> pdb=" O ALA A3352 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A3357 " --> pdb=" O GLU A3353 " (cutoff:3.500A) Processing helix chain 'A' and resid 3364 through 3388 removed outlier: 3.868A pdb=" N LEU A3370 " --> pdb=" O ASN A3366 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A3380 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A3381 " --> pdb=" O SER A3377 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A3382 " --> pdb=" O TRP A3378 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A3385 " --> pdb=" O LEU A3381 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A3388 " --> pdb=" O ARG A3384 " (cutoff:3.500A) Processing helix chain 'A' and resid 3392 through 3397 Processing helix chain 'A' and resid 3404 through 3412 removed outlier: 3.745A pdb=" N GLU A3410 " --> pdb=" O PHE A3406 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A3411 " --> pdb=" O TYR A3407 " (cutoff:3.500A) Processing helix chain 'A' and resid 3412 through 3417 Processing helix chain 'A' and resid 3428 through 3441 removed outlier: 3.513A pdb=" N SER A3433 " --> pdb=" O THR A3429 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A3437 " --> pdb=" O SER A3433 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A3438 " --> pdb=" O SER A3434 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A3439 " --> pdb=" O LEU A3435 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A3441 " --> pdb=" O LEU A3437 " (cutoff:3.500A) Processing helix chain 'A' and resid 3447 through 3463 removed outlier: 3.787A pdb=" N LEU A3453 " --> pdb=" O ALA A3449 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A3455 " --> pdb=" O LEU A3451 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA A3456 " --> pdb=" O ASP A3452 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS A3460 " --> pdb=" O ALA A3456 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A3461 " --> pdb=" O PHE A3457 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A3462 " --> pdb=" O TYR A3458 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3484 removed outlier: 3.832A pdb=" N ASN A3477 " --> pdb=" O GLY A3473 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR A3478 " --> pdb=" O LEU A3474 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A3479 " --> pdb=" O LEU A3475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A3482 " --> pdb=" O THR A3478 " (cutoff:3.500A) Processing helix chain 'A' and resid 3485 through 3511 removed outlier: 3.606A pdb=" N ASN A3495 " --> pdb=" O GLU A3491 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A3496 " --> pdb=" O ARG A3492 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS A3498 " --> pdb=" O THR A3494 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A3499 " --> pdb=" O ASN A3495 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A3500 " --> pdb=" O GLY A3496 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS A3502 " --> pdb=" O LYS A3498 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU A3503 " --> pdb=" O SER A3499 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A3507 " --> pdb=" O GLU A3503 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A3509 " --> pdb=" O ASP A3505 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A3511 " --> pdb=" O ILE A3507 " (cutoff:3.500A) Processing helix chain 'A' and resid 3517 through 3544 removed outlier: 3.514A pdb=" N LEU A3521 " --> pdb=" O ASN A3517 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A3522 " --> pdb=" O VAL A3518 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A3523 " --> pdb=" O ASP A3519 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A3526 " --> pdb=" O LYS A3522 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A3527 " --> pdb=" O GLN A3523 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A3528 " --> pdb=" O SER A3524 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A3531 " --> pdb=" O LYS A3527 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR A3533 " --> pdb=" O HIS A3529 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A3534 " --> pdb=" O ASN A3530 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A3535 " --> pdb=" O ASN A3531 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A3541 " --> pdb=" O ARG A3537 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A3542 " --> pdb=" O LYS A3538 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A3543 " --> pdb=" O TYR A3539 " (cutoff:3.500A) Processing helix chain 'A' and resid 3547 through 3554 removed outlier: 3.711A pdb=" N ILE A3551 " --> pdb=" O ALA A3547 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A3554 " --> pdb=" O ILE A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3586 removed outlier: 3.754A pdb=" N UNK A3584 " --> pdb=" O UNK A3580 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N UNK A3585 " --> pdb=" O UNK A3581 " (cutoff:3.500A) Processing helix chain 'A' and resid 3603 through 3617 removed outlier: 3.715A pdb=" N ASN A3607 " --> pdb=" O THR A3603 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A3609 " --> pdb=" O ALA A3605 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A3613 " --> pdb=" O ASP A3609 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS A3614 " --> pdb=" O SER A3610 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A3615 " --> pdb=" O TYR A3611 " (cutoff:3.500A) Processing helix chain 'A' and resid 3623 through 3640 removed outlier: 3.678A pdb=" N PHE A3630 " --> pdb=" O LEU A3626 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A3640 " --> pdb=" O ARG A3636 " (cutoff:3.500A) Processing helix chain 'A' and resid 3653 through 3674 removed outlier: 3.589A pdb=" N THR A3658 " --> pdb=" O ALA A3654 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A3659 " --> pdb=" O TYR A3655 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A3663 " --> pdb=" O GLN A3659 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A3668 " --> pdb=" O LEU A3664 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3690 through 3695 removed outlier: 3.684A pdb=" N ILE A3694 " --> pdb=" O SER A3690 " (cutoff:3.500A) Processing helix chain 'A' and resid 3706 through 3712 removed outlier: 3.594A pdb=" N ASP A3710 " --> pdb=" O ASN A3707 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE A3712 " --> pdb=" O SER A3709 " (cutoff:3.500A) Processing helix chain 'A' and resid 3719 through 3727 removed outlier: 3.629A pdb=" N ARG A3724 " --> pdb=" O LEU A3720 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A3726 " --> pdb=" O LYS A3722 " (cutoff:3.500A) Processing helix chain 'A' and resid 3737 through 3755 removed outlier: 3.666A pdb=" N ALA A3744 " --> pdb=" O GLU A3740 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A3747 " --> pdb=" O MET A3743 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A3748 " --> pdb=" O ALA A3744 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A3749 " --> pdb=" O LEU A3745 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A3755 " --> pdb=" O PHE A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3756 through 3780 removed outlier: 3.521A pdb=" N CYS A3768 " --> pdb=" O THR A3764 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A3769 " --> pdb=" O ASN A3765 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A3775 " --> pdb=" O ASN A3771 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A3776 " --> pdb=" O GLY A3772 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS A3779 " --> pdb=" O LEU A3775 " (cutoff:3.500A) Processing helix chain 'A' and resid 3792 through 3805 removed outlier: 3.664A pdb=" N ASP A3797 " --> pdb=" O LYS A3793 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A3798 " --> pdb=" O ALA A3794 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A3802 " --> pdb=" O ASN A3798 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A3804 " --> pdb=" O ARG A3800 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP A3805 " --> pdb=" O LEU A3801 " (cutoff:3.500A) Processing helix chain 'A' and resid 3805 through 3822 removed outlier: 3.772A pdb=" N ASP A3811 " --> pdb=" O PRO A3807 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A3815 " --> pdb=" O ASP A3811 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A3816 " --> pdb=" O TYR A3812 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A3817 " --> pdb=" O ALA A3813 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER A3818 " --> pdb=" O ALA A3814 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A3822 " --> pdb=" O SER A3818 " (cutoff:3.500A) Processing helix chain 'A' and resid 3827 through 3829 No H-bonds generated for 'chain 'A' and resid 3827 through 3829' Processing helix chain 'A' and resid 3830 through 3839 removed outlier: 4.037A pdb=" N ALA A3836 " --> pdb=" O ILE A3832 " (cutoff:3.500A) Processing helix chain 'A' and resid 3840 through 3845 removed outlier: 3.976A pdb=" N VAL A3845 " --> pdb=" O SER A3841 " (cutoff:3.500A) Processing helix chain 'A' and resid 3854 through 3856 No H-bonds generated for 'chain 'A' and resid 3854 through 3856' Processing helix chain 'A' and resid 3857 through 3878 removed outlier: 4.342A pdb=" N ARG A3863 " --> pdb=" O GLU A3859 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A3869 " --> pdb=" O GLU A3865 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A3873 " --> pdb=" O ASN A3869 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A3876 " --> pdb=" O LEU A3872 " (cutoff:3.500A) Processing helix chain 'A' and resid 3884 through 3896 removed outlier: 4.315A pdb=" N ILE A3889 " --> pdb=" O PHE A3885 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE A3890 " --> pdb=" O VAL A3886 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3925 removed outlier: 3.628A pdb=" N THR A3922 " --> pdb=" O ALA A3918 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE A3923 " --> pdb=" O PHE A3919 " (cutoff:3.500A) Processing helix chain 'A' and resid 3927 through 3936 removed outlier: 3.625A pdb=" N LYS A3932 " --> pdb=" O LEU A3928 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A3933 " --> pdb=" O SER A3929 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A3934 " --> pdb=" O PHE A3930 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP A3936 " --> pdb=" O LYS A3932 " (cutoff:3.500A) Processing helix chain 'A' and resid 3948 through 3964 removed outlier: 3.528A pdb=" N SER A3952 " --> pdb=" O TRP A3948 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A3953 " --> pdb=" O LEU A3949 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS A3954 " --> pdb=" O SER A3950 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET A3957 " --> pdb=" O PHE A3953 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A3961 " --> pdb=" O MET A3957 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A3963 " --> pdb=" O ASN A3959 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A3964 " --> pdb=" O VAL A3960 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3981 removed outlier: 3.533A pdb=" N SER A3969 " --> pdb=" O SER A3965 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A3970 " --> pdb=" O SER A3966 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU A3973 " --> pdb=" O SER A3969 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A3978 " --> pdb=" O THR A3974 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A3979 " --> pdb=" O ALA A3975 " (cutoff:3.500A) Processing helix chain 'A' and resid 3992 through 3997 removed outlier: 3.737A pdb=" N SER A3997 " --> pdb=" O LYS A3993 " (cutoff:3.500A) Processing helix chain 'A' and resid 3999 through 4007 removed outlier: 3.566A pdb=" N ILE A4003 " --> pdb=" O THR A3999 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG A4005 " --> pdb=" O PRO A4001 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4041 removed outlier: 3.872A pdb=" N VAL A4013 " --> pdb=" O ALA A4009 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A4015 " --> pdb=" O THR A4011 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A4019 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A4021 " --> pdb=" O SER A4017 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A4026 " --> pdb=" O THR A4022 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A4033 " --> pdb=" O TYR A4029 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A4034 " --> pdb=" O ILE A4030 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 339 removed outlier: 6.344A pdb=" N MET A 312 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA3, first strand: chain 'A' and resid 673 through 677 removed outlier: 6.545A pdb=" N LEU A 674 " --> pdb=" O LEU A 827 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP A 829 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 676 " --> pdb=" O ASP A 829 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU A 650 " --> pdb=" O ALA A 875 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET A 877 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 652 " --> pdb=" O MET A 877 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 649 " --> pdb=" O THR A 897 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AA5, first strand: chain 'A' and resid 1106 through 1108 removed outlier: 4.037A pdb=" N VAL A1148 " --> pdb=" O ARG A1106 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A1147 " --> pdb=" O PHE A1191 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR A1193 " --> pdb=" O ILE A1147 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A1149 " --> pdb=" O THR A1193 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A1194 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A1217 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1173 through 1175 removed outlier: 3.895A pdb=" N LEU A1173 " --> pdb=" O VAL A1182 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A1182 " --> pdb=" O LEU A1173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1488 through 1492 removed outlier: 3.668A pdb=" N PHE A1489 " --> pdb=" O GLN A1534 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A1536 " --> pdb=" O PHE A1489 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1769 through 1770 removed outlier: 6.317A pdb=" N ARG A1770 " --> pdb=" O LEU A1813 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A1812 " --> pdb=" O PHE A1856 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ALA A1858 " --> pdb=" O VAL A1812 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A1814 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2006 through 2008 removed outlier: 3.537A pdb=" N VAL A2006 " --> pdb=" O ALA A2013 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A2008 " --> pdb=" O GLU A2011 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A2011 " --> pdb=" O ILE A2008 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2075 through 2079 removed outlier: 3.607A pdb=" N ILE A2210 " --> pdb=" O ASP A2076 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU A2209 " --> pdb=" O PHE A2259 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR A2261 " --> pdb=" O LEU A2209 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A2211 " --> pdb=" O THR A2261 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A2050 " --> pdb=" O LEU A2260 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N MET A2262 " --> pdb=" O LEU A2050 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU A2052 " --> pdb=" O MET A2262 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2090 through 2094 removed outlier: 4.447A pdb=" N GLY A2092 " --> pdb=" O PHE A2195 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A2195 " --> pdb=" O GLY A2092 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A2193 " --> pdb=" O GLU A2094 " (cutoff:3.500A) 854 hydrogen bonds defined for protein. 2496 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: 5.04 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.16: 1 1.16 - 1.33: 4159 1.33 - 1.49: 9221 1.49 - 1.65: 9592 1.65 - 1.81: 57 Bond restraints: 23030 Sorted by residual: bond pdb=" C SER A 462 " pdb=" N GLU A 463 " ideal model delta sigma weight residual 1.332 1.747 -0.414 1.40e-02 5.10e+03 8.76e+02 bond pdb=" C PRO A1934 " pdb=" N TRP A1935 " ideal model delta sigma weight residual 1.334 1.004 0.330 1.25e-02 6.40e+03 6.96e+02 bond pdb=" C LEU A4000 " pdb=" N PRO A4001 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.32e+00 bond pdb=" C TRP A3312 " pdb=" N PRO A3313 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.29e+00 bond pdb=" C UNK A 30 " pdb=" N UNK A 31 " ideal model delta sigma weight residual 1.329 1.358 -0.029 1.40e-02 5.10e+03 4.20e+00 ... (remaining 23025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.81: 31555 13.81 - 27.62: 3 27.62 - 41.42: 1 41.42 - 55.23: 0 55.23 - 69.04: 1 Bond angle restraints: 31560 Sorted by residual: angle pdb=" O SER A 462 " pdb=" C SER A 462 " pdb=" N GLU A 463 " ideal model delta sigma weight residual 122.59 53.55 69.04 1.33e+00 5.65e-01 2.69e+03 angle pdb=" O PRO A1934 " pdb=" C PRO A1934 " pdb=" N TRP A1935 " ideal model delta sigma weight residual 122.64 93.06 29.58 1.35e+00 5.49e-01 4.80e+02 angle pdb=" C PRO A1934 " pdb=" N TRP A1935 " pdb=" CA TRP A1935 " ideal model delta sigma weight residual 122.23 145.51 -23.28 1.54e+00 4.22e-01 2.29e+02 angle pdb=" CA PRO A1934 " pdb=" C PRO A1934 " pdb=" N TRP A1935 " ideal model delta sigma weight residual 116.70 141.51 -24.81 2.07e+00 2.33e-01 1.44e+02 angle pdb=" C ASN A2753 " pdb=" N TYR A2754 " pdb=" CA TYR A2754 " ideal model delta sigma weight residual 121.80 135.72 -13.92 2.44e+00 1.68e-01 3.25e+01 ... (remaining 31555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 13243 15.25 - 30.50: 314 30.50 - 45.75: 68 45.75 - 61.00: 9 61.00 - 76.25: 5 Dihedral angle restraints: 13639 sinusoidal: 3102 harmonic: 10537 Sorted by residual: dihedral pdb=" CA TRP A3312 " pdb=" C TRP A3312 " pdb=" N PRO A3313 " pdb=" CA PRO A3313 " ideal model delta harmonic sigma weight residual -180.00 -133.44 -46.56 0 5.00e+00 4.00e-02 8.67e+01 dihedral pdb=" CA LYS A 734 " pdb=" C LYS A 734 " pdb=" N ASN A 735 " pdb=" CA ASN A 735 " ideal model delta harmonic sigma weight residual 180.00 -147.18 -32.82 0 5.00e+00 4.00e-02 4.31e+01 dihedral pdb=" CA ASP A3515 " pdb=" C ASP A3515 " pdb=" N VAL A3516 " pdb=" CA VAL A3516 " ideal model delta harmonic sigma weight residual -180.00 -147.69 -32.31 0 5.00e+00 4.00e-02 4.18e+01 ... (remaining 13636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3106 0.053 - 0.106: 768 0.106 - 0.159: 87 0.159 - 0.212: 12 0.212 - 0.264: 2 Chirality restraints: 3975 Sorted by residual: chirality pdb=" CB ILE A2948 " pdb=" CA ILE A2948 " pdb=" CG1 ILE A2948 " pdb=" CG2 ILE A2948 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE A2613 " pdb=" CA ILE A2613 " pdb=" CG1 ILE A2613 " pdb=" CG2 ILE A2613 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TRP A3312 " pdb=" N TRP A3312 " pdb=" C TRP A3312 " pdb=" CB TRP A3312 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3972 not shown) Planarity restraints: 4158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 462 " -0.186 2.00e-02 2.50e+03 2.73e-01 7.47e+02 pdb=" C SER A 462 " 0.441 2.00e-02 2.50e+03 pdb=" O SER A 462 " -0.264 2.00e-02 2.50e+03 pdb=" N GLU A 463 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1934 " 0.037 2.00e-02 2.50e+03 6.43e-02 4.13e+01 pdb=" C PRO A1934 " -0.111 2.00e-02 2.50e+03 pdb=" O PRO A1934 " 0.026 2.00e-02 2.50e+03 pdb=" N TRP A1935 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A3312 " 0.056 5.00e-02 4.00e+02 8.64e-02 1.19e+01 pdb=" N PRO A3313 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO A3313 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A3313 " 0.047 5.00e-02 4.00e+02 ... (remaining 4155 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 5 1.80 - 2.58: 102 2.58 - 3.35: 26725 3.35 - 4.13: 45149 4.13 - 4.90: 81362 Nonbonded interactions: 153343 Sorted by model distance: nonbonded pdb=" OG SER A2352 " pdb=" ND2 ASN A2943 " model vdw 1.027 3.120 nonbonded pdb=" CG2 THR A2290 " pdb=" OD2 ASP A2951 " model vdw 1.311 3.460 nonbonded pdb=" CA TYR A1055 " pdb=" CB ARG A1232 " model vdw 1.598 3.870 nonbonded pdb=" CD1 LEU A2465 " pdb=" CE1 TYR A2544 " model vdw 1.636 3.760 nonbonded pdb=" OE1 GLN A2344 " pdb=" CG1 VAL A2947 " model vdw 1.667 3.460 ... (remaining 153338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.610 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.190 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 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 1.019 23031 Z= 0.741 Angle : 0.890 69.039 31560 Z= 0.535 Chirality : 0.046 0.264 3975 Planarity : 0.006 0.273 4158 Dihedral : 8.224 76.253 6729 Min Nonbonded Distance : 1.027 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.45 % Favored : 93.25 % Rotamer: Outliers : 0.50 % Allowed : 1.98 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.06 % 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: -6.25 (0.09), residues: 3304 helix: -4.88 (0.03), residues: 1626 sheet: -2.15 (0.35), residues: 189 loop : -3.41 (0.13), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2470 TYR 0.024 0.001 TYR A2005 PHE 0.026 0.002 PHE A2594 TRP 0.030 0.002 TRP A2836 HIS 0.007 0.001 HIS A2844 Details of bonding type rmsd covalent geometry : bond 0.00476 (23030) covalent geometry : angle 0.89039 (31560) hydrogen bonds : bond 0.34289 ( 854) hydrogen bonds : angle 9.64087 ( 2496) Misc. bond : bond 1.01938 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 438 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2008 ILE cc_start: 0.9304 (mt) cc_final: 0.8846 (mm) REVERT: A 2027 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7770 (tp) REVERT: A 2037 TYR cc_start: 0.8544 (m-80) cc_final: 0.8304 (m-80) REVERT: A 2044 ILE cc_start: 0.8865 (pt) cc_final: 0.8662 (mm) REVERT: A 2452 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7981 (mtmm) REVERT: A 2519 CYS cc_start: 0.6409 (m) cc_final: 0.6166 (t) REVERT: A 2534 THR cc_start: 0.4744 (p) cc_final: 0.4472 (t) REVERT: A 2599 LEU cc_start: 0.6255 (mp) cc_final: 0.5708 (tt) REVERT: A 2918 ILE cc_start: 0.6029 (mm) cc_final: 0.5815 (mm) outliers start: 7 outliers final: 1 residues processed: 445 average time/residue: 0.1513 time to fit residues: 102.9995 Evaluate side-chains 214 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 212 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0000 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2010 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2598 ASN A2611 HIS A2844 HIS A2936 ASN A2943 ASN A3011 ASN ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3462 GLN A3476 HIS A3484 GLN A3529 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.085666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.069778 restraints weight = 135494.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.070887 restraints weight = 91913.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.071526 restraints weight = 64560.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.071728 restraints weight = 55747.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.071916 restraints weight = 47732.938| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 23031 Z= 0.124 Angle : 0.570 10.132 31560 Z= 0.305 Chirality : 0.041 0.187 3975 Planarity : 0.004 0.082 4158 Dihedral : 4.263 41.949 3692 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.53 (0.11), residues: 3304 helix: -3.19 (0.08), residues: 1645 sheet: -1.48 (0.37), residues: 190 loop : -2.89 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2394 TYR 0.021 0.001 TYR A2005 PHE 0.024 0.001 PHE A3780 TRP 0.045 0.002 TRP A3386 HIS 0.007 0.001 HIS A3846 Details of bonding type rmsd covalent geometry : bond 0.00248 (23030) covalent geometry : angle 0.57011 (31560) hydrogen bonds : bond 0.04883 ( 854) hydrogen bonds : angle 4.67499 ( 2496) Misc. bond : bond 0.00095 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.820 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: A 376 VAL cc_start: 0.9068 (t) cc_final: 0.8835 (p) REVERT: A 2028 PHE cc_start: 0.7985 (p90) cc_final: 0.7725 (p90) REVERT: A 2044 ILE cc_start: 0.8847 (pt) cc_final: 0.8622 (mm) REVERT: A 2212 ASP cc_start: 0.7790 (t0) cc_final: 0.7423 (t0) REVERT: A 2331 TYR cc_start: 0.7891 (m-10) cc_final: 0.7605 (m-10) REVERT: A 2473 LEU cc_start: 0.8497 (tp) cc_final: 0.8144 (tp) REVERT: A 2519 CYS cc_start: 0.7692 (m) cc_final: 0.6884 (t) REVERT: A 2599 LEU cc_start: 0.7250 (mp) cc_final: 0.6440 (tt) REVERT: A 2744 LEU cc_start: 0.8373 (pp) cc_final: 0.7961 (pp) REVERT: A 2826 MET cc_start: 0.7747 (tmm) cc_final: 0.7473 (tmm) REVERT: A 2989 MET cc_start: 0.8438 (mmp) cc_final: 0.8165 (mmm) REVERT: A 3136 PHE cc_start: 0.8283 (t80) cc_final: 0.8045 (t80) REVERT: A 3623 PHE cc_start: 0.8252 (t80) cc_final: 0.7958 (t80) REVERT: A 3633 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7986 (mm-30) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1411 time to fit residues: 59.3465 Evaluate side-chains 172 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 280 optimal weight: 9.9990 chunk 342 optimal weight: 0.7980 chunk 357 optimal weight: 0.8980 chunk 319 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 187 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 328 optimal weight: 0.6980 chunk 276 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 ASN A2651 GLN A3028 HIS A3340 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.082121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066749 restraints weight = 136722.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.066818 restraints weight = 102125.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066752 restraints weight = 75786.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.066883 restraints weight = 76923.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.066993 restraints weight = 67905.755| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23031 Z= 0.129 Angle : 0.546 9.277 31560 Z= 0.290 Chirality : 0.040 0.175 3975 Planarity : 0.004 0.082 4158 Dihedral : 3.983 39.868 3692 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.13), residues: 3304 helix: -1.43 (0.12), residues: 1662 sheet: -1.35 (0.36), residues: 197 loop : -2.63 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A3450 TYR 0.024 0.001 TYR A2005 PHE 0.025 0.001 PHE A 874 TRP 0.044 0.002 TRP A2579 HIS 0.005 0.001 HIS A2369 Details of bonding type rmsd covalent geometry : bond 0.00276 (23030) covalent geometry : angle 0.54610 (31560) hydrogen bonds : bond 0.03448 ( 854) hydrogen bonds : angle 3.77668 ( 2496) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.9036 (t) cc_final: 0.8810 (p) REVERT: A 453 TRP cc_start: 0.7921 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: A 2028 PHE cc_start: 0.8284 (p90) cc_final: 0.8060 (p90) REVERT: A 2044 ILE cc_start: 0.9013 (pt) cc_final: 0.8679 (mt) REVERT: A 2331 TYR cc_start: 0.8051 (m-10) cc_final: 0.7772 (m-10) REVERT: A 2473 LEU cc_start: 0.8257 (tp) cc_final: 0.8046 (tp) REVERT: A 2519 CYS cc_start: 0.7868 (m) cc_final: 0.7076 (t) REVERT: A 2599 LEU cc_start: 0.7440 (mp) cc_final: 0.6650 (tt) REVERT: A 2826 MET cc_start: 0.7774 (tmm) cc_final: 0.7261 (tmm) REVERT: A 2944 VAL cc_start: 0.7294 (t) cc_final: 0.7072 (t) REVERT: A 2989 MET cc_start: 0.8531 (mmp) cc_final: 0.8242 (tpp) REVERT: A 2996 MET cc_start: 0.8537 (mmm) cc_final: 0.8301 (mmm) REVERT: A 3135 ILE cc_start: 0.9589 (mp) cc_final: 0.9280 (mt) REVERT: A 3345 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8263 (mt-10) REVERT: A 3383 LEU cc_start: 0.9227 (mp) cc_final: 0.9026 (pp) REVERT: A 3523 GLN cc_start: 0.6998 (mp-120) cc_final: 0.6625 (mp10) REVERT: A 3542 LEU cc_start: 0.8899 (pp) cc_final: 0.8690 (mm) REVERT: A 3705 TYR cc_start: 0.8207 (m-10) cc_final: 0.7912 (m-10) REVERT: A 3795 ASN cc_start: 0.9427 (m-40) cc_final: 0.9182 (m110) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.1117 time to fit residues: 39.9889 Evaluate side-chains 148 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 65 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 325 optimal weight: 5.9990 chunk 279 optimal weight: 0.0970 chunk 320 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 242 optimal weight: 0.7980 chunk 340 optimal weight: 0.9990 chunk 353 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2820 ASN ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.081010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.065582 restraints weight = 134214.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.065318 restraints weight = 102483.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065513 restraints weight = 75285.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.065605 restraints weight = 73252.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065739 restraints weight = 67120.616| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23031 Z= 0.111 Angle : 0.507 10.495 31560 Z= 0.267 Chirality : 0.040 0.171 3975 Planarity : 0.003 0.081 4158 Dihedral : 3.857 38.904 3692 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.14), residues: 3304 helix: -0.47 (0.13), residues: 1680 sheet: -0.96 (0.37), residues: 199 loop : -2.46 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3323 TYR 0.023 0.001 TYR A2005 PHE 0.016 0.001 PHE A3763 TRP 0.050 0.002 TRP A2579 HIS 0.004 0.001 HIS A2369 Details of bonding type rmsd covalent geometry : bond 0.00234 (23030) covalent geometry : angle 0.50693 (31560) hydrogen bonds : bond 0.02763 ( 854) hydrogen bonds : angle 3.47927 ( 2496) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.9051 (t) cc_final: 0.8780 (p) REVERT: A 2028 PHE cc_start: 0.8235 (p90) cc_final: 0.7953 (p90) REVERT: A 2331 TYR cc_start: 0.8104 (m-10) cc_final: 0.7872 (m-10) REVERT: A 2473 LEU cc_start: 0.8269 (tp) cc_final: 0.8055 (tp) REVERT: A 2519 CYS cc_start: 0.8091 (m) cc_final: 0.7215 (t) REVERT: A 2599 LEU cc_start: 0.7294 (mp) cc_final: 0.6650 (tt) REVERT: A 2715 ASP cc_start: 0.7519 (m-30) cc_final: 0.7267 (t70) REVERT: A 2944 VAL cc_start: 0.7652 (t) cc_final: 0.7435 (t) REVERT: A 2996 MET cc_start: 0.8522 (mmm) cc_final: 0.8245 (mmm) REVERT: A 3135 ILE cc_start: 0.9554 (mp) cc_final: 0.9319 (mm) REVERT: A 3345 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8297 (mt-10) REVERT: A 3523 GLN cc_start: 0.7126 (mp-120) cc_final: 0.6773 (mp10) REVERT: A 3542 LEU cc_start: 0.8848 (pp) cc_final: 0.8631 (mm) REVERT: A 3608 MET cc_start: 0.8135 (tpp) cc_final: 0.7830 (tpt) REVERT: A 3694 ILE cc_start: 0.7629 (mm) cc_final: 0.7413 (pt) REVERT: A 3705 TYR cc_start: 0.8143 (m-10) cc_final: 0.7890 (m-10) REVERT: A 3777 LEU cc_start: 0.8660 (mm) cc_final: 0.8345 (mm) REVERT: A 3795 ASN cc_start: 0.9476 (m-40) cc_final: 0.9249 (m110) REVERT: A 3843 PHE cc_start: 0.7582 (m-80) cc_final: 0.7182 (m-80) REVERT: A 4006 TYR cc_start: 0.7593 (t80) cc_final: 0.6964 (t80) REVERT: A 4028 MET cc_start: 0.9072 (tpt) cc_final: 0.8748 (tpt) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1141 time to fit residues: 38.6709 Evaluate side-chains 149 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 194 optimal weight: 7.9990 chunk 142 optimal weight: 0.4980 chunk 317 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 321 optimal weight: 2.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2670 ASN A2820 ASN A3028 HIS A3340 GLN A3477 ASN A3529 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.073801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.058849 restraints weight = 136638.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.058232 restraints weight = 105881.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058514 restraints weight = 83426.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.058663 restraints weight = 74129.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058730 restraints weight = 67192.567| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 23031 Z= 0.335 Angle : 0.852 11.706 31560 Z= 0.448 Chirality : 0.048 0.196 3975 Planarity : 0.005 0.090 4158 Dihedral : 5.606 40.512 3692 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.08 % Favored : 90.80 % Rotamer: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.14), residues: 3304 helix: -0.65 (0.12), residues: 1713 sheet: -1.15 (0.39), residues: 175 loop : -2.64 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A3017 TYR 0.049 0.003 TYR A2752 PHE 0.031 0.003 PHE A2666 TRP 0.065 0.004 TRP A 381 HIS 0.013 0.003 HIS A2611 Details of bonding type rmsd covalent geometry : bond 0.00694 (23030) covalent geometry : angle 0.85162 (31560) hydrogen bonds : bond 0.04404 ( 854) hydrogen bonds : angle 4.90044 ( 2496) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2473 LEU cc_start: 0.8605 (tp) cc_final: 0.8163 (tp) REVERT: A 2599 LEU cc_start: 0.7999 (mp) cc_final: 0.6910 (tt) REVERT: A 2715 ASP cc_start: 0.8047 (m-30) cc_final: 0.7778 (t0) REVERT: A 2826 MET cc_start: 0.8636 (ttt) cc_final: 0.7860 (tmm) REVERT: A 3345 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8230 (mt-10) REVERT: A 3523 GLN cc_start: 0.7387 (mp-120) cc_final: 0.6989 (mp10) REVERT: A 3542 LEU cc_start: 0.8976 (pp) cc_final: 0.8773 (mm) REVERT: A 3694 ILE cc_start: 0.7743 (mm) cc_final: 0.7422 (pt) REVERT: A 3705 TYR cc_start: 0.8446 (m-10) cc_final: 0.8154 (m-80) REVERT: A 3773 MET cc_start: 0.8802 (mtp) cc_final: 0.8522 (mtt) REVERT: A 3774 MET cc_start: 0.7668 (tmm) cc_final: 0.7338 (ptm) REVERT: A 4006 TYR cc_start: 0.7878 (t80) cc_final: 0.7417 (t80) REVERT: A 4007 TYR cc_start: 0.7945 (t80) cc_final: 0.7220 (t80) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.1106 time to fit residues: 31.2353 Evaluate side-chains 120 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 210 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 223 optimal weight: 0.0870 chunk 298 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 277 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2820 ASN A2943 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.075564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.061851 restraints weight = 137106.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.061126 restraints weight = 142122.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.061356 restraints weight = 126818.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.061499 restraints weight = 108110.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.061625 restraints weight = 90471.302| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23031 Z= 0.140 Angle : 0.567 10.039 31560 Z= 0.298 Chirality : 0.041 0.176 3975 Planarity : 0.003 0.086 4158 Dihedral : 4.646 41.660 3692 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.81 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.15), residues: 3304 helix: 0.08 (0.13), residues: 1718 sheet: -1.21 (0.38), residues: 174 loop : -2.55 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3017 TYR 0.020 0.001 TYR A2005 PHE 0.014 0.001 PHE A2601 TRP 0.034 0.002 TRP A 381 HIS 0.006 0.001 HIS A2018 Details of bonding type rmsd covalent geometry : bond 0.00306 (23030) covalent geometry : angle 0.56746 (31560) hydrogen bonds : bond 0.02954 ( 854) hydrogen bonds : angle 3.96070 ( 2496) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.9042 (t) cc_final: 0.8736 (p) REVERT: A 2212 ASP cc_start: 0.8371 (t0) cc_final: 0.8033 (t0) REVERT: A 2519 CYS cc_start: 0.7824 (m) cc_final: 0.6981 (t) REVERT: A 2599 LEU cc_start: 0.7673 (mp) cc_final: 0.6892 (tt) REVERT: A 2715 ASP cc_start: 0.7636 (m-30) cc_final: 0.7352 (t0) REVERT: A 2826 MET cc_start: 0.8505 (ttt) cc_final: 0.7761 (tmm) REVERT: A 2989 MET cc_start: 0.8721 (mmp) cc_final: 0.8476 (tpp) REVERT: A 3107 MET cc_start: 0.7442 (mmm) cc_final: 0.7200 (mmm) REVERT: A 3345 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7958 (mt-10) REVERT: A 3474 LEU cc_start: 0.8929 (mt) cc_final: 0.8628 (tt) REVERT: A 3523 GLN cc_start: 0.7263 (mp-120) cc_final: 0.6926 (mp10) REVERT: A 3774 MET cc_start: 0.7544 (tmm) cc_final: 0.7282 (ppp) REVERT: A 3795 ASN cc_start: 0.9383 (m110) cc_final: 0.9005 (m-40) REVERT: A 4006 TYR cc_start: 0.7124 (t80) cc_final: 0.6887 (t80) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1140 time to fit residues: 32.4229 Evaluate side-chains 132 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 102 optimal weight: 10.0000 chunk 264 optimal weight: 0.8980 chunk 350 optimal weight: 6.9990 chunk 122 optimal weight: 30.0000 chunk 170 optimal weight: 0.0040 chunk 254 optimal weight: 0.7980 chunk 163 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 262 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 overall best weight: 2.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2045 ASN A2639 ASN A2820 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.074230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059450 restraints weight = 136826.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058700 restraints weight = 115588.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.058935 restraints weight = 92590.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059164 restraints weight = 77453.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.059202 restraints weight = 69098.155| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23031 Z= 0.191 Angle : 0.622 10.204 31560 Z= 0.327 Chirality : 0.042 0.174 3975 Planarity : 0.004 0.090 4158 Dihedral : 4.730 41.457 3692 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.99 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.15), residues: 3304 helix: 0.21 (0.13), residues: 1754 sheet: -1.25 (0.37), residues: 183 loop : -2.58 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 821 TYR 0.029 0.002 TYR A2752 PHE 0.020 0.002 PHE A3923 TRP 0.050 0.003 TRP A 381 HIS 0.006 0.001 HIS A2369 Details of bonding type rmsd covalent geometry : bond 0.00409 (23030) covalent geometry : angle 0.62223 (31560) hydrogen bonds : bond 0.03190 ( 854) hydrogen bonds : angle 4.10737 ( 2496) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2212 ASP cc_start: 0.8430 (t0) cc_final: 0.8047 (t0) REVERT: A 2395 LEU cc_start: 0.9033 (tt) cc_final: 0.8825 (tp) REVERT: A 2519 CYS cc_start: 0.7830 (m) cc_final: 0.7016 (t) REVERT: A 2599 LEU cc_start: 0.7696 (mp) cc_final: 0.6895 (tt) REVERT: A 2663 MET cc_start: 0.8062 (mmt) cc_final: 0.7764 (mmt) REVERT: A 2715 ASP cc_start: 0.7769 (m-30) cc_final: 0.7419 (t0) REVERT: A 2826 MET cc_start: 0.8539 (ttt) cc_final: 0.7898 (tmm) REVERT: A 3107 MET cc_start: 0.7481 (mmm) cc_final: 0.7252 (mmm) REVERT: A 3345 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8116 (mt-10) REVERT: A 3474 LEU cc_start: 0.9102 (mt) cc_final: 0.8781 (tp) REVERT: A 3523 GLN cc_start: 0.7458 (mp-120) cc_final: 0.7091 (mp10) REVERT: A 3774 MET cc_start: 0.7444 (tmm) cc_final: 0.7236 (ppp) REVERT: A 3795 ASN cc_start: 0.9434 (m110) cc_final: 0.9042 (m-40) REVERT: A 4006 TYR cc_start: 0.7602 (t80) cc_final: 0.7320 (t80) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1056 time to fit residues: 27.9898 Evaluate side-chains 122 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 39 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 268 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2676 ASN A2820 ASN ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3523 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.074979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.060136 restraints weight = 134283.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.059555 restraints weight = 105387.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059767 restraints weight = 86786.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.060016 restraints weight = 73112.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.060092 restraints weight = 64639.737| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.7213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23031 Z= 0.121 Angle : 0.544 9.517 31560 Z= 0.284 Chirality : 0.041 0.171 3975 Planarity : 0.003 0.085 4158 Dihedral : 4.376 41.536 3692 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.23 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.15), residues: 3304 helix: 0.57 (0.13), residues: 1750 sheet: -0.94 (0.37), residues: 202 loop : -2.35 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 821 TYR 0.016 0.001 TYR A2754 PHE 0.015 0.001 PHE A3780 TRP 0.033 0.002 TRP A 381 HIS 0.003 0.001 HIS A2369 Details of bonding type rmsd covalent geometry : bond 0.00265 (23030) covalent geometry : angle 0.54390 (31560) hydrogen bonds : bond 0.02648 ( 854) hydrogen bonds : angle 3.74754 ( 2496) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.9086 (t) cc_final: 0.8789 (p) REVERT: A 2212 ASP cc_start: 0.8319 (t0) cc_final: 0.7978 (t0) REVERT: A 2519 CYS cc_start: 0.7673 (m) cc_final: 0.7117 (t) REVERT: A 2599 LEU cc_start: 0.7388 (mp) cc_final: 0.6839 (tt) REVERT: A 2715 ASP cc_start: 0.7683 (m-30) cc_final: 0.7301 (t0) REVERT: A 2826 MET cc_start: 0.8466 (ttt) cc_final: 0.7827 (tmm) REVERT: A 3107 MET cc_start: 0.7516 (mmm) cc_final: 0.7278 (mmm) REVERT: A 3345 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 3474 LEU cc_start: 0.9135 (mt) cc_final: 0.8746 (tp) REVERT: A 3523 GLN cc_start: 0.7415 (mp10) cc_final: 0.7004 (mp10) REVERT: A 3751 PHE cc_start: 0.7940 (t80) cc_final: 0.7696 (t80) REVERT: A 3795 ASN cc_start: 0.9424 (m110) cc_final: 0.9057 (m-40) REVERT: A 4006 TYR cc_start: 0.7683 (t80) cc_final: 0.7307 (t80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1149 time to fit residues: 31.8536 Evaluate side-chains 126 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 243 optimal weight: 2.9990 chunk 337 optimal weight: 0.9980 chunk 319 optimal weight: 0.9990 chunk 324 optimal weight: 0.9990 chunk 315 optimal weight: 20.0000 chunk 295 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 347 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 356 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2820 ASN A3530 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.074486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060071 restraints weight = 136861.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059142 restraints weight = 122293.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.059466 restraints weight = 101602.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.059660 restraints weight = 83867.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.059735 restraints weight = 73546.198| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.7472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23031 Z= 0.150 Angle : 0.589 14.361 31560 Z= 0.306 Chirality : 0.041 0.170 3975 Planarity : 0.003 0.090 4158 Dihedral : 4.394 41.443 3692 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.32 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.15), residues: 3304 helix: 0.67 (0.13), residues: 1762 sheet: -0.94 (0.37), residues: 197 loop : -2.33 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A3017 TYR 0.018 0.002 TYR A2975 PHE 0.025 0.002 PHE A3923 TRP 0.043 0.002 TRP A 381 HIS 0.006 0.001 HIS A2369 Details of bonding type rmsd covalent geometry : bond 0.00328 (23030) covalent geometry : angle 0.58890 (31560) hydrogen bonds : bond 0.02775 ( 854) hydrogen bonds : angle 3.78366 ( 2496) Misc. bond : bond 0.00931 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.9107 (t) cc_final: 0.8799 (p) REVERT: A 2212 ASP cc_start: 0.8368 (t0) cc_final: 0.7998 (t0) REVERT: A 2324 MET cc_start: 0.8145 (mmm) cc_final: 0.7875 (mmm) REVERT: A 2519 CYS cc_start: 0.7758 (m) cc_final: 0.7190 (t) REVERT: A 2599 LEU cc_start: 0.7509 (mp) cc_final: 0.6930 (tt) REVERT: A 2663 MET cc_start: 0.7981 (mmt) cc_final: 0.7629 (mmt) REVERT: A 2715 ASP cc_start: 0.7721 (m-30) cc_final: 0.7404 (t0) REVERT: A 2826 MET cc_start: 0.8465 (ttt) cc_final: 0.7874 (tmm) REVERT: A 3107 MET cc_start: 0.7416 (mmm) cc_final: 0.7154 (mmm) REVERT: A 3204 ASP cc_start: 0.8570 (m-30) cc_final: 0.8363 (p0) REVERT: A 3345 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8218 (mt-10) REVERT: A 3474 LEU cc_start: 0.9064 (mt) cc_final: 0.8795 (tp) REVERT: A 3523 GLN cc_start: 0.7833 (mp10) cc_final: 0.7233 (mp10) REVERT: A 3774 MET cc_start: 0.7626 (ppp) cc_final: 0.7348 (ppp) REVERT: A 3795 ASN cc_start: 0.9407 (m110) cc_final: 0.9035 (m-40) REVERT: A 4006 TYR cc_start: 0.7691 (t80) cc_final: 0.7377 (t80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1120 time to fit residues: 30.1456 Evaluate side-chains 124 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 3 optimal weight: 6.9990 chunk 254 optimal weight: 0.5980 chunk 257 optimal weight: 0.6980 chunk 341 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 268 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 226 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 320 optimal weight: 0.0570 chunk 345 optimal weight: 0.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2716 ASN A2820 ASN A3340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.075820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.063285 restraints weight = 137072.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.062398 restraints weight = 184689.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.062703 restraints weight = 160481.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.062543 restraints weight = 125304.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.062555 restraints weight = 116191.293| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.7452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23031 Z= 0.094 Angle : 0.530 15.580 31560 Z= 0.276 Chirality : 0.040 0.173 3975 Planarity : 0.003 0.084 4158 Dihedral : 4.148 39.957 3692 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 0.07 % Allowed : 0.50 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.16), residues: 3304 helix: 0.92 (0.13), residues: 1763 sheet: -0.83 (0.38), residues: 200 loop : -2.24 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2945 TYR 0.014 0.001 TYR A2005 PHE 0.026 0.001 PHE A3751 TRP 0.023 0.001 TRP A 381 HIS 0.004 0.001 HIS A2369 Details of bonding type rmsd covalent geometry : bond 0.00205 (23030) covalent geometry : angle 0.53026 (31560) hydrogen bonds : bond 0.02415 ( 854) hydrogen bonds : angle 3.45093 ( 2496) Misc. bond : bond 0.01182 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.8982 (t) cc_final: 0.8707 (p) REVERT: A 2212 ASP cc_start: 0.8194 (t0) cc_final: 0.7917 (t0) REVERT: A 2324 MET cc_start: 0.8025 (mmm) cc_final: 0.7751 (mmm) REVERT: A 2395 LEU cc_start: 0.8998 (tt) cc_final: 0.8791 (tt) REVERT: A 2519 CYS cc_start: 0.7461 (m) cc_final: 0.7051 (t) REVERT: A 2599 LEU cc_start: 0.7246 (mp) cc_final: 0.6955 (tt) REVERT: A 2715 ASP cc_start: 0.7439 (m-30) cc_final: 0.7162 (t0) REVERT: A 2716 ASN cc_start: 0.9606 (OUTLIER) cc_final: 0.9406 (t0) REVERT: A 2826 MET cc_start: 0.8290 (ttt) cc_final: 0.7677 (tmm) REVERT: A 3107 MET cc_start: 0.7265 (mmm) cc_final: 0.7041 (mmm) REVERT: A 3345 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8035 (mt-10) REVERT: A 3474 LEU cc_start: 0.8901 (mt) cc_final: 0.8653 (tp) REVERT: A 3523 GLN cc_start: 0.7623 (mp10) cc_final: 0.7030 (mp10) REVERT: A 4028 MET cc_start: 0.9130 (tpt) cc_final: 0.8917 (tpt) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.1132 time to fit residues: 33.5207 Evaluate side-chains 127 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 272 optimal weight: 0.9980 chunk 260 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 351 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 316 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2716 ASN A2820 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.075482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.061104 restraints weight = 136836.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.060213 restraints weight = 125454.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.060651 restraints weight = 95847.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.060805 restraints weight = 77775.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.060890 restraints weight = 70862.492| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.7574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23031 Z= 0.105 Angle : 0.520 8.760 31560 Z= 0.270 Chirality : 0.040 0.176 3975 Planarity : 0.003 0.086 4158 Dihedral : 3.999 39.257 3692 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.51 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.16), residues: 3304 helix: 1.06 (0.13), residues: 1772 sheet: -0.73 (0.37), residues: 209 loop : -2.16 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2945 TYR 0.021 0.001 TYR A3767 PHE 0.028 0.001 PHE A3923 TRP 0.031 0.002 TRP A 381 HIS 0.005 0.001 HIS A2369 Details of bonding type rmsd covalent geometry : bond 0.00232 (23030) covalent geometry : angle 0.52005 (31560) hydrogen bonds : bond 0.02424 ( 854) hydrogen bonds : angle 3.44649 ( 2496) Misc. bond : bond 0.00040 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3049.70 seconds wall clock time: 53 minutes 15.63 seconds (3195.63 seconds total)