Starting phenix.real_space_refine on Tue Mar 19 01:52:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i26_0328/03_2024/6i26_0328_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i26_0328/03_2024/6i26_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_0328/03_2024/6i26_0328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i26_0328/03_2024/6i26_0328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i26_0328/03_2024/6i26_0328_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i26_0328/03_2024/6i26_0328_neut.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 14329 2.51 5 N 4101 2.21 5 O 4303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.04, per 1000 atoms: 0.53 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: 9.01 Conformation dependent library (CDL) restraints added in 4.6 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: 5.46 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: 14.67 Time building geometry restraints manager: 9.84 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 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: 3.320 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: 12.250 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 69.020 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 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 % Allowed : 1.98 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.06 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A2836 HIS 0.007 0.001 HIS A2844 PHE 0.026 0.002 PHE A2594 TYR 0.024 0.001 TYR A2005 ARG 0.004 0.001 ARG A2470 *********************** 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 : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2008 ILE cc_start: 0.9304 (mt) cc_final: 0.8844 (mm) REVERT: A 2027 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7768 (tp) REVERT: A 2037 TYR cc_start: 0.8544 (m-80) cc_final: 0.8305 (m-80) REVERT: A 2044 ILE cc_start: 0.8865 (pt) cc_final: 0.8657 (mm) REVERT: A 2205 LYS cc_start: 0.8729 (mttm) cc_final: 0.8370 (tttt) REVERT: A 2452 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7981 (mtmm) REVERT: A 2519 CYS cc_start: 0.6409 (m) cc_final: 0.6164 (t) REVERT: A 2534 THR cc_start: 0.4744 (p) cc_final: 0.4473 (t) REVERT: A 2599 LEU cc_start: 0.6255 (mp) cc_final: 0.5710 (tt) REVERT: A 2918 ILE cc_start: 0.6029 (mm) cc_final: 0.5815 (mm) outliers start: 7 outliers final: 1 residues processed: 445 average time/residue: 0.3601 time to fit residues: 244.9950 Evaluate side-chains 212 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 210 time to evaluate : 2.429 ------------------------------------------------------------------------------- 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: 2.9990 chunk 208 optimal weight: 3.9990 chunk 325 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 ** A2943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3011 ASN A3028 HIS ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3462 GLN A3476 HIS A3484 GLN A3529 HIS A3789 HIS A3848 ASN A3883 ASN A4036 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23030 Z= 0.230 Angle : 0.636 9.978 31560 Z= 0.340 Chirality : 0.042 0.164 3975 Planarity : 0.005 0.089 4158 Dihedral : 4.584 41.915 3692 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.23 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: -4.36 (0.12), residues: 3304 helix: -2.98 (0.09), residues: 1654 sheet: -1.63 (0.36), residues: 197 loop : -2.85 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A3386 HIS 0.007 0.002 HIS A3846 PHE 0.021 0.002 PHE A3780 TYR 0.024 0.002 TYR A2005 ARG 0.010 0.001 ARG A3150 *********************** 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 233 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.9135 (t) cc_final: 0.8922 (p) REVERT: A 2087 MET cc_start: 0.7686 (mmt) cc_final: 0.7477 (mmm) REVERT: A 2205 LYS cc_start: 0.8729 (mttm) cc_final: 0.8210 (tttt) REVERT: A 2331 TYR cc_start: 0.8800 (m-10) cc_final: 0.8576 (m-10) REVERT: A 2452 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8156 (mtmm) REVERT: A 2559 GLU cc_start: 0.6898 (pp20) cc_final: 0.6453 (tm-30) REVERT: A 2599 LEU cc_start: 0.6700 (mp) cc_final: 0.5892 (tt) REVERT: A 2826 MET cc_start: 0.7480 (tmm) cc_final: 0.7189 (tmm) REVERT: A 3117 MET cc_start: 0.7919 (mmm) cc_final: 0.7595 (mtt) REVERT: A 3136 PHE cc_start: 0.7649 (t80) cc_final: 0.7382 (t80) REVERT: A 3754 ILE cc_start: 0.6783 (mt) cc_final: 0.6468 (mt) REVERT: A 3774 MET cc_start: 0.5424 (ppp) cc_final: 0.5148 (tmm) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3252 time to fit residues: 123.6413 Evaluate side-chains 154 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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: 30.0000 chunk 270 optimal weight: 0.8980 chunk 221 optimal weight: 0.0870 chunk 89 optimal weight: 20.0000 chunk 325 optimal weight: 0.0050 chunk 351 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 322 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 overall best weight: 0.5572 ------------------------------------------------------------------------------- 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** ** A2943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3044 ASN ** A3262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3789 HIS A3848 ASN A3883 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 23030 Z= 0.129 Angle : 0.491 9.761 31560 Z= 0.260 Chirality : 0.039 0.151 3975 Planarity : 0.003 0.086 4158 Dihedral : 3.939 39.873 3692 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 0.14 % Allowed : 2.26 % Favored : 97.59 % 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: -2.95 (0.13), residues: 3304 helix: -1.46 (0.11), residues: 1669 sheet: -1.33 (0.36), residues: 200 loop : -2.61 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 381 HIS 0.004 0.001 HIS A3846 PHE 0.012 0.001 PHE A3058 TYR 0.023 0.001 TYR A2005 ARG 0.004 0.000 ARG A3636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.9129 (t) cc_final: 0.8891 (p) REVERT: A 2044 ILE cc_start: 0.9186 (pt) cc_final: 0.8921 (mm) REVERT: A 2212 ASP cc_start: 0.8556 (t0) cc_final: 0.8088 (t0) REVERT: A 2452 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8191 (mtmm) REVERT: A 2519 CYS cc_start: 0.6859 (m) cc_final: 0.6589 (t) REVERT: A 2599 LEU cc_start: 0.6565 (mp) cc_final: 0.6103 (tt) REVERT: A 3135 ILE cc_start: 0.9312 (mp) cc_final: 0.8941 (mm) outliers start: 2 outliers final: 0 residues processed: 211 average time/residue: 0.2874 time to fit residues: 103.4565 Evaluate side-chains 145 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.467 ------------------------------------------------------------------------------- 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: 1.9990 chunk 244 optimal weight: 0.0770 chunk 169 optimal weight: 0.0870 chunk 36 optimal weight: 8.9990 chunk 155 optimal weight: 0.3980 chunk 218 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 346 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 309 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2207 HIS A2531 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3262 ASN ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3883 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4231 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= 0.116 Angle : 0.468 8.794 31560 Z= 0.247 Chirality : 0.039 0.164 3975 Planarity : 0.003 0.085 4158 Dihedral : 3.733 38.680 3692 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer: Outliers : 0.07 % Allowed : 2.41 % Favored : 97.52 % 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 (0.14), residues: 3304 helix: -0.47 (0.13), residues: 1675 sheet: -1.04 (0.37), residues: 200 loop : -2.49 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 381 HIS 0.003 0.001 HIS A2611 PHE 0.017 0.001 PHE A3780 TYR 0.022 0.001 TYR A2005 ARG 0.002 0.000 ARG A2224 *********************** 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 201 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.9127 (t) cc_final: 0.8882 (p) REVERT: A 2044 ILE cc_start: 0.9214 (pt) cc_final: 0.8959 (mm) REVERT: A 2212 ASP cc_start: 0.8559 (t0) cc_final: 0.8007 (t0) REVERT: A 2452 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8243 (mtmm) REVERT: A 2519 CYS cc_start: 0.6933 (m) cc_final: 0.6634 (t) REVERT: A 2599 LEU cc_start: 0.6531 (mp) cc_final: 0.6319 (tt) REVERT: A 2996 MET cc_start: 0.7663 (mmm) cc_final: 0.7234 (mmm) REVERT: A 3135 ILE cc_start: 0.9280 (mp) cc_final: 0.8973 (mm) REVERT: A 3754 ILE cc_start: 0.6699 (mt) cc_final: 0.6408 (mt) REVERT: A 3774 MET cc_start: 0.5401 (ppp) cc_final: 0.5061 (tmm) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2818 time to fit residues: 97.2303 Evaluate side-chains 149 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.167 ------------------------------------------------------------------------------- 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: 0.6980 chunk 196 optimal weight: 0.0060 chunk 5 optimal weight: 8.9990 chunk 257 optimal weight: 1.9990 chunk 142 optimal weight: 0.0570 chunk 295 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 310 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 overall best weight: 0.9518 ------------------------------------------------------------------------------- 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** ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3484 GLN A3883 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 23030 Z= 0.156 Angle : 0.489 8.792 31560 Z= 0.257 Chirality : 0.039 0.156 3975 Planarity : 0.003 0.083 4158 Dihedral : 3.717 37.709 3692 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 0.14 % Allowed : 2.12 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (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: -1.35 (0.15), residues: 3304 helix: 0.22 (0.13), residues: 1699 sheet: -0.75 (0.38), residues: 202 loop : -2.37 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 825 HIS 0.004 0.001 HIS A2369 PHE 0.023 0.001 PHE A2681 TYR 0.022 0.001 TYR A2005 ARG 0.004 0.000 ARG A2945 *********************** 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 191 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.9038 (t) cc_final: 0.8784 (p) REVERT: A 2212 ASP cc_start: 0.8681 (t0) cc_final: 0.8173 (t0) REVERT: A 2452 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8378 (mtmm) REVERT: A 2599 LEU cc_start: 0.6987 (mp) cc_final: 0.6592 (tt) REVERT: A 2663 MET cc_start: 0.7236 (mmt) cc_final: 0.6692 (mmp) REVERT: A 3135 ILE cc_start: 0.9262 (mp) cc_final: 0.8952 (mm) REVERT: A 3777 LEU cc_start: 0.6729 (mm) cc_final: 0.6412 (mm) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.2853 time to fit residues: 94.0045 Evaluate side-chains 138 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.539 ------------------------------------------------------------------------------- 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: 0.0370 chunk 311 optimal weight: 2.9990 chunk 68 optimal weight: 30.0000 chunk 203 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 346 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- 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 ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3262 ASN A3544 ASN A3789 HIS A3883 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23030 Z= 0.254 Angle : 0.585 10.038 31560 Z= 0.310 Chirality : 0.041 0.297 3975 Planarity : 0.003 0.082 4158 Dihedral : 4.238 37.685 3692 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % 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: -1.20 (0.15), residues: 3304 helix: 0.40 (0.13), residues: 1717 sheet: -0.81 (0.38), residues: 196 loop : -2.38 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 381 HIS 0.007 0.001 HIS A2369 PHE 0.021 0.002 PHE A2681 TYR 0.024 0.002 TYR A2005 ARG 0.004 0.001 ARG A2945 *********************** 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: 1 poor density : 172 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.8970 (t) cc_final: 0.8682 (p) REVERT: A 2452 LYS cc_start: 0.9287 (mmtt) cc_final: 0.8670 (mtmt) REVERT: A 2599 LEU cc_start: 0.6883 (mp) cc_final: 0.6538 (tt) REVERT: A 2996 MET cc_start: 0.7765 (mmm) cc_final: 0.7271 (mmm) REVERT: A 3135 ILE cc_start: 0.9337 (mp) cc_final: 0.9078 (mm) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.2732 time to fit residues: 82.0388 Evaluate side-chains 127 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.543 ------------------------------------------------------------------------------- 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: 8.9990 chunk 39 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 252 optimal weight: 0.3980 chunk 195 optimal weight: 0.7980 chunk 291 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 345 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** ** A2716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3028 HIS ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3436 ASN A3529 HIS A3883 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23030 Z= 0.204 Angle : 0.555 11.714 31560 Z= 0.290 Chirality : 0.041 0.150 3975 Planarity : 0.003 0.082 4158 Dihedral : 4.192 38.526 3692 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.84 % Favored : 93.07 % Rotamer: Outliers : 0.07 % Allowed : 2.19 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (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: -0.89 (0.15), residues: 3304 helix: 0.68 (0.13), residues: 1723 sheet: -0.73 (0.37), residues: 198 loop : -2.27 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 381 HIS 0.005 0.001 HIS A2018 PHE 0.023 0.001 PHE A3923 TYR 0.038 0.002 TYR A4007 ARG 0.006 0.001 ARG A3467 *********************** 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 162 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.8964 (t) cc_final: 0.8675 (p) REVERT: A 2212 ASP cc_start: 0.8494 (t0) cc_final: 0.7798 (t0) REVERT: A 2519 CYS cc_start: 0.7132 (m) cc_final: 0.6547 (t) REVERT: A 2996 MET cc_start: 0.7672 (mmm) cc_final: 0.7116 (mmm) REVERT: A 3135 ILE cc_start: 0.9364 (mp) cc_final: 0.9077 (mm) REVERT: A 3474 LEU cc_start: 0.7826 (mt) cc_final: 0.7582 (tt) REVERT: A 3930 PHE cc_start: 0.5434 (t80) cc_final: 0.5127 (t80) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2760 time to fit residues: 79.5539 Evaluate side-chains 123 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.548 ------------------------------------------------------------------------------- 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: 2.9990 chunk 137 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 271 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A2790 ASN A2943 ASN ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4023 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23030 Z= 0.179 Angle : 0.529 10.942 31560 Z= 0.276 Chirality : 0.040 0.189 3975 Planarity : 0.003 0.082 4158 Dihedral : 4.066 37.655 3692 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.23 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.65 (0.16), residues: 3304 helix: 0.86 (0.13), residues: 1735 sheet: -0.67 (0.38), residues: 179 loop : -2.15 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 381 HIS 0.005 0.001 HIS A2018 PHE 0.013 0.001 PHE A2594 TYR 0.039 0.002 TYR A4007 ARG 0.006 0.000 ARG A2976 *********************** 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 166 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.8969 (t) cc_final: 0.8678 (p) REVERT: A 2212 ASP cc_start: 0.8487 (t0) cc_final: 0.7819 (t0) REVERT: A 2519 CYS cc_start: 0.6935 (m) cc_final: 0.6467 (t) REVERT: A 3135 ILE cc_start: 0.9347 (mp) cc_final: 0.9096 (mm) REVERT: A 3474 LEU cc_start: 0.7987 (mt) cc_final: 0.7724 (tt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2711 time to fit residues: 80.6980 Evaluate side-chains 127 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.508 ------------------------------------------------------------------------------- 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: 0.7980 chunk 330 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 321 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 252 optimal weight: 0.6980 chunk 98 optimal weight: 0.0870 chunk 290 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 320 optimal weight: 0.0070 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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** A2716 ASN ** A3222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.6677 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= 0.120 Angle : 0.495 9.968 31560 Z= 0.254 Chirality : 0.039 0.158 3975 Planarity : 0.003 0.081 4158 Dihedral : 3.793 37.377 3692 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 0.07 % Allowed : 0.50 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % 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: -0.37 (0.16), residues: 3304 helix: 1.11 (0.14), residues: 1741 sheet: -0.51 (0.38), residues: 190 loop : -2.06 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 381 HIS 0.003 0.001 HIS A2018 PHE 0.026 0.001 PHE A3923 TYR 0.025 0.001 TYR A2005 ARG 0.003 0.000 ARG A2945 *********************** 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 173 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.8965 (t) cc_final: 0.8681 (p) REVERT: A 2212 ASP cc_start: 0.8576 (t0) cc_final: 0.7939 (t0) REVERT: A 2405 MET cc_start: 0.8420 (mpp) cc_final: 0.8189 (mtm) REVERT: A 2519 CYS cc_start: 0.6855 (m) cc_final: 0.6524 (t) REVERT: A 3050 TYR cc_start: 0.8673 (m-10) cc_final: 0.8456 (m-10) REVERT: A 3051 ILE cc_start: 0.9460 (pt) cc_final: 0.8960 (pt) REVERT: A 3135 ILE cc_start: 0.9322 (mp) cc_final: 0.9094 (mm) REVERT: A 3474 LEU cc_start: 0.8005 (mt) cc_final: 0.7738 (tt) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.2771 time to fit residues: 84.8371 Evaluate side-chains 129 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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: 0.5980 chunk 340 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 161 optimal weight: 0.0670 chunk 236 optimal weight: 0.4980 chunk 356 optimal weight: 4.9990 chunk 328 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 29 optimal weight: 0.0020 chunk 219 optimal weight: 0.4980 chunk 174 optimal weight: 0.0570 overall best weight: 0.2244 ------------------------------------------------------------------------------- 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 A3702 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.6722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23030 Z= 0.111 Angle : 0.486 9.534 31560 Z= 0.249 Chirality : 0.039 0.187 3975 Planarity : 0.003 0.080 4158 Dihedral : 3.590 35.328 3692 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.20 % Favored : 93.77 % Rotamer: Outliers : 0.07 % Allowed : 0.35 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (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: 1741 sheet: -0.42 (0.38), residues: 194 loop : -1.93 (0.18), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A3893 HIS 0.005 0.001 HIS A3028 PHE 0.015 0.001 PHE A2594 TYR 0.029 0.001 TYR A2005 ARG 0.002 0.000 ARG A2945 ********************** 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 177 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 VAL cc_start: 0.8959 (t) cc_final: 0.8679 (p) REVERT: A 2212 ASP cc_start: 0.8524 (t0) cc_final: 0.7934 (t0) REVERT: A 2519 CYS cc_start: 0.6881 (m) cc_final: 0.6591 (t) REVERT: A 3135 ILE cc_start: 0.9322 (mp) cc_final: 0.9086 (mm) REVERT: A 3474 LEU cc_start: 0.7983 (mt) cc_final: 0.7609 (tt) REVERT: A 3774 MET cc_start: 0.5075 (pmm) cc_final: 0.4622 (ptp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.2796 time to fit residues: 86.5731 Evaluate side-chains 132 residues out of total 3050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 2.620 ------------------------------------------------------------------------------- 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: 7.9990 chunk 302 optimal weight: 2.9990 chunk 87 optimal weight: 0.0470 chunk 261 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 292 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2045 ASN A2531 ASN ** A2545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3436 ASN A3765 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.075654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.060203 restraints weight = 135679.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.060641 restraints weight = 94398.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.061170 restraints weight = 64502.933| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23030 Z= 0.214 Angle : 0.569 10.495 31560 Z= 0.294 Chirality : 0.041 0.180 3975 Planarity : 0.003 0.082 4158 Dihedral : 3.980 36.639 3692 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.92 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.16), residues: 3304 helix: 1.39 (0.14), residues: 1729 sheet: -0.35 (0.39), residues: 188 loop : -1.94 (0.18), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A2897 HIS 0.011 0.001 HIS A3028 PHE 0.030 0.002 PHE A3751 TYR 0.030 0.002 TYR A4007 ARG 0.003 0.001 ARG A3323 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3826.81 seconds wall clock time: 69 minutes 42.04 seconds (4182.04 seconds total)