Starting phenix.real_space_refine (version: dev) on Fri Feb 24 10:16:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i26_0328/02_2023/6i26_0328_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i26_0328/02_2023/6i26_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i26_0328/02_2023/6i26_0328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i26_0328/02_2023/6i26_0328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i26_0328/02_2023/6i26_0328_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i26_0328/02_2023/6i26_0328_neut.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A ARG 1944": "NH1" <-> "NH2" Residue "A TYR 2005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2274": "NH1" <-> "NH2" Residue "A ARG 2609": "NH1" <-> "NH2" Residue "A ARG 3323": "NH1" <-> "NH2" Residue "A ARG 3964": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 22765 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 22765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3587, 22765 Classifications: {'peptide': 3587} Incomplete info: {'truncation_to_alanine': 1858} Link IDs: {'CIS': 1, 'PTRANS': 111, 'TRANS': 3474} Chain breaks: 35 Unresolved chain link angles: 67 Unresolved non-hydrogen bonds: 6080 Unresolved non-hydrogen angles: 7831 Unresolved non-hydrogen dihedrals: 4827 Unresolved non-hydrogen chiralities: 554 Planarities with less than four sites: {'GLN:plan1': 57, 'ARG:plan': 79, 'TYR:plan': 31, 'UNK:plan-1': 221, 'TRP:plan': 16, 'ASP:plan': 116, 'ASN:plan1': 103, 'PHE:plan': 81, 'GLU:plan': 155, 'HIS:plan': 32} Unresolved non-hydrogen planarities: 3128 Time building chain proxies: 13.04, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.17 Conformation dependent library (CDL) restraints added in 4.0 seconds 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: 3.99 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: 13.53 Time building geometry restraints manager: 9.95 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: 53.55 - 71.94: 1 71.94 - 90.34: 0 90.34 - 108.73: 764 108.73 - 127.12: 30654 127.12 - 145.51: 141 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: 0.41 - 1.31: 3 1.31 - 2.21: 24 2.21 - 3.10: 13688 3.10 - 4.00: 51869 4.00 - 4.90: 87763 Warning: very small nonbonded interaction distances. Nonbonded interactions: 153347 Sorted by model distance: nonbonded pdb=" CB PHE A2292 " pdb=" NZ LYS A2946 " model vdw 0.411 3.520 nonbonded pdb=" OG SER A2352 " pdb=" ND2 ASN A2943 " model vdw 1.027 2.520 nonbonded pdb=" CG PHE A2292 " pdb=" NZ LYS A2946 " model vdw 1.178 3.340 nonbonded pdb=" CG2 THR A2290 " pdb=" OD2 ASP A2951 " model vdw 1.311 3.460 nonbonded pdb=" CB PHE A2292 " pdb=" CE LYS A2946 " model vdw 1.596 3.840 ... (remaining 153342 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 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. 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: 2.870 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: 0.020 Extract box with map and model: 13.270 Check model and map are aligned: 0.350 Process input model: 66.520 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 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 : 0.005 0.414 23030 Z= 0.306 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 : 0.411 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.45 % Favored : 93.25 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 7 poor density : 438 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 445 average time/residue: 0.3704 time to fit residues: 252.2302 Evaluate side-chains 208 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2395 time to fit residues: 3.8543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 183 optimal weight: 0.0970 chunk 144 optimal weight: 30.0000 chunk 280 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 325 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2413 ASN A2531 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2598 ASN A2611 HIS A2844 HIS A2936 ASN ** A2943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3011 ASN ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3462 GLN A3476 HIS A3484 GLN A3529 HIS A3789 HIS A3883 ASN A4036 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 23030 Z= 0.206 Angle : 0.603 9.632 31560 Z= 0.323 Chirality : 0.041 0.157 3975 Planarity : 0.005 0.088 4158 Dihedral : 4.344 41.850 3692 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.72 % Favored : 94.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.12), residues: 3304 helix: -2.99 (0.09), residues: 1643 sheet: -1.60 (0.37), residues: 185 loop : -2.87 (0.15), residues: 1476 *********************** 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 243 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3339 time to fit residues: 130.4642 Evaluate side-chains 148 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.632 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 270 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 325 optimal weight: 0.9980 chunk 351 optimal weight: 0.6980 chunk 290 optimal weight: 1.9990 chunk 322 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2531 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2598 ASN ** A2943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3024 GLN A3028 HIS A3044 ASN ** A3262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3789 HIS A3883 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 23030 Z= 0.144 Angle : 0.509 10.625 31560 Z= 0.271 Chirality : 0.039 0.151 3975 Planarity : 0.003 0.086 4158 Dihedral : 3.913 39.767 3692 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.18 % Favored : 94.76 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.14), residues: 3304 helix: -1.36 (0.12), residues: 1672 sheet: -1.31 (0.36), residues: 200 loop : -2.60 (0.15), residues: 1432 *********************** 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 208 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 206 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.3036 time to fit residues: 107.5855 Evaluate side-chains 141 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 326 optimal weight: 0.4980 chunk 346 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2531 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3028 HIS ** A3262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3484 GLN ** A3789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3883 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 23030 Z= 0.257 Angle : 0.621 11.766 31560 Z= 0.329 Chirality : 0.042 0.188 3975 Planarity : 0.004 0.086 4158 Dihedral : 4.492 38.854 3692 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.20 % Favored : 92.68 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.15), residues: 3304 helix: -0.50 (0.13), residues: 1697 sheet: -0.97 (0.38), residues: 193 loop : -2.49 (0.16), residues: 1414 *********************** 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 179 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 179 average time/residue: 0.2973 time to fit residues: 91.3376 Evaluate side-chains 129 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 2.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 257 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 chunk 239 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 176 optimal weight: 0.0870 chunk 310 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2531 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2943 ASN A3544 ASN ** A3789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3883 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 23030 Z= 0.188 Angle : 0.540 10.038 31560 Z= 0.283 Chirality : 0.040 0.157 3975 Planarity : 0.003 0.084 4158 Dihedral : 4.167 38.519 3692 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 3304 helix: 0.10 (0.13), residues: 1714 sheet: -1.03 (0.38), residues: 196 loop : -2.35 (0.17), residues: 1394 *********************** 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 170 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.3132 time to fit residues: 90.9700 Evaluate side-chains 133 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.632 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 30.0000 chunk 311 optimal weight: 0.9980 chunk 68 optimal weight: 30.0000 chunk 203 optimal weight: 0.0570 chunk 85 optimal weight: 0.9990 chunk 346 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2531 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2790 ASN A3789 HIS A3883 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 23030 Z= 0.150 Angle : 0.507 9.514 31560 Z= 0.265 Chirality : 0.040 0.166 3975 Planarity : 0.003 0.084 4158 Dihedral : 3.989 37.871 3692 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.31 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3304 helix: 0.56 (0.13), residues: 1714 sheet: -0.85 (0.37), residues: 196 loop : -2.25 (0.17), residues: 1394 *********************** 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 173 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.2971 time to fit residues: 89.1673 Evaluate side-chains 134 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 1.9990 chunk 39 optimal weight: 0.0030 chunk 197 optimal weight: 3.9990 chunk 252 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 291 optimal weight: 10.0000 chunk 193 optimal weight: 0.6980 chunk 345 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 210 optimal weight: 0.0170 chunk 159 optimal weight: 7.9990 overall best weight: 0.5028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2531 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2676 ASN A2716 ASN ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3340 GLN A3883 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 23030 Z= 0.119 Angle : 0.487 12.317 31560 Z= 0.253 Chirality : 0.039 0.155 3975 Planarity : 0.003 0.083 4158 Dihedral : 3.820 37.475 3692 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.87 % Favored : 94.07 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 3304 helix: 0.85 (0.14), residues: 1717 sheet: -0.71 (0.37), residues: 196 loop : -2.11 (0.17), residues: 1391 *********************** 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 172 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 172 average time/residue: 0.3060 time to fit residues: 90.6378 Evaluate side-chains 130 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.813 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 0.0970 chunk 137 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2531 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3340 GLN A3436 ASN A3529 HIS A3883 ASN A3971 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23030 Z= 0.182 Angle : 0.526 11.557 31560 Z= 0.274 Chirality : 0.040 0.158 3975 Planarity : 0.003 0.084 4158 Dihedral : 3.959 37.423 3692 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.20 % Favored : 92.71 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 3304 helix: 0.91 (0.13), residues: 1729 sheet: -0.57 (0.38), residues: 188 loop : -2.08 (0.17), residues: 1387 *********************** 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 159 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.2950 time to fit residues: 83.6770 Evaluate side-chains 121 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 0.0870 chunk 330 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 321 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 chunk 98 optimal weight: 0.0060 chunk 290 optimal weight: 0.9990 chunk 304 optimal weight: 0.7980 chunk 320 optimal weight: 0.8980 overall best weight: 0.5174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2531 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3436 ASN ** A3702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3971 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 23030 Z= 0.119 Angle : 0.489 10.826 31560 Z= 0.253 Chirality : 0.039 0.195 3975 Planarity : 0.003 0.082 4158 Dihedral : 3.754 37.216 3692 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 3304 helix: 1.14 (0.14), residues: 1731 sheet: -0.41 (0.38), residues: 188 loop : -1.99 (0.17), residues: 1385 *********************** 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 170 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.488 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2958 time to fit residues: 87.2733 Evaluate side-chains 126 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 0.0980 chunk 340 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 161 optimal weight: 0.0020 chunk 236 optimal weight: 0.0020 chunk 356 optimal weight: 1.9990 chunk 328 optimal weight: 0.4980 chunk 284 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 219 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2531 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3436 ASN A3544 ASN ** A3702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3703 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.6704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 23030 Z= 0.107 Angle : 0.488 10.489 31560 Z= 0.248 Chirality : 0.039 0.169 3975 Planarity : 0.003 0.084 4158 Dihedral : 3.565 35.917 3692 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.81 % Favored : 94.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 3304 helix: 1.34 (0.14), residues: 1726 sheet: -0.38 (0.38), residues: 202 loop : -1.92 (0.18), residues: 1376 ********************** 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 175 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3146 time to fit residues: 96.4599 Evaluate side-chains 131 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 0.0970 chunk 302 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 261 optimal weight: 0.0000 chunk 41 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 284 optimal weight: 0.4980 chunk 119 optimal weight: 20.0000 chunk 292 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2531 ASN A3044 ASN ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3436 ASN ** A3702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3703 ASN A3707 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.078221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.064861 restraints weight = 137999.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.063940 restraints weight = 151944.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.064437 restraints weight = 130259.206| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 23030 Z= 0.109 Angle : 0.481 10.616 31560 Z= 0.244 Chirality : 0.039 0.183 3975 Planarity : 0.003 0.083 4158 Dihedral : 3.481 35.939 3692 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.78 % Favored : 94.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 3304 helix: 1.47 (0.14), residues: 1740 sheet: -0.23 (0.39), residues: 192 loop : -1.89 (0.18), residues: 1372 =============================================================================== Job complete usr+sys time: 3637.36 seconds wall clock time: 66 minutes 39.52 seconds (3999.52 seconds total)