Starting phenix.real_space_refine on Wed Mar 20 18:59:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lht_23350/03_2024/7lht_23350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lht_23350/03_2024/7lht_23350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lht_23350/03_2024/7lht_23350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lht_23350/03_2024/7lht_23350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lht_23350/03_2024/7lht_23350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lht_23350/03_2024/7lht_23350.pdb" } resolution = 3.5 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= 0.006 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 178 5.16 5 C 18037 2.51 5 N 4873 2.21 5 O 5147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 601": "OE1" <-> "OE2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "A ARG 793": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1067": "NH1" <-> "NH2" Residue "A GLU 1100": "OE1" <-> "OE2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A GLU 1146": "OE1" <-> "OE2" Residue "A ARG 1161": "NH1" <-> "NH2" Residue "A GLU 1190": "OE1" <-> "OE2" Residue "A ARG 1199": "NH1" <-> "NH2" Residue "A ARG 1223": "NH1" <-> "NH2" Residue "A ARG 1246": "NH1" <-> "NH2" Residue "A GLU 1263": "OE1" <-> "OE2" Residue "A ARG 1282": "NH1" <-> "NH2" Residue "A GLU 1301": "OE1" <-> "OE2" Residue "A ARG 1325": "NH1" <-> "NH2" Residue "A ARG 1381": "NH1" <-> "NH2" Residue "A ARG 1386": "NH1" <-> "NH2" Residue "A ARG 1412": "NH1" <-> "NH2" Residue "A GLU 1427": "OE1" <-> "OE2" Residue "A ARG 1441": "NH1" <-> "NH2" Residue "A ARG 1483": "NH1" <-> "NH2" Residue "A GLU 1507": "OE1" <-> "OE2" Residue "A GLU 1531": "OE1" <-> "OE2" Residue "A GLU 1537": "OE1" <-> "OE2" Residue "A ARG 1538": "NH1" <-> "NH2" Residue "A ARG 1550": "NH1" <-> "NH2" Residue "A ARG 1558": "NH1" <-> "NH2" Residue "A GLU 1566": "OE1" <-> "OE2" Residue "A GLU 1578": "OE1" <-> "OE2" Residue "A ARG 1629": "NH1" <-> "NH2" Residue "A GLU 1654": "OE1" <-> "OE2" Residue "A ARG 1677": "NH1" <-> "NH2" Residue "A ARG 1711": "NH1" <-> "NH2" Residue "A ARG 1731": "NH1" <-> "NH2" Residue "A GLU 1760": "OE1" <-> "OE2" Residue "A GLU 1790": "OE1" <-> "OE2" Residue "A GLU 1797": "OE1" <-> "OE2" Residue "A GLU 1805": "OE1" <-> "OE2" Residue "A ARG 1847": "NH1" <-> "NH2" Residue "A GLU 1874": "OE1" <-> "OE2" Residue "A GLU 1876": "OE1" <-> "OE2" Residue "A GLU 1878": "OE1" <-> "OE2" Residue "A PHE 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1901": "OE1" <-> "OE2" Residue "A ARG 1915": "NH1" <-> "NH2" Residue "A ARG 1918": "NH1" <-> "NH2" Residue "A ARG 1943": "NH1" <-> "NH2" Residue "A ARG 1957": "NH1" <-> "NH2" Residue "A ARG 1968": "NH1" <-> "NH2" Residue "A ARG 1973": "NH1" <-> "NH2" Residue "A ARG 1983": "NH1" <-> "NH2" Residue "A ARG 2026": "NH1" <-> "NH2" Residue "A ARG 2039": "NH1" <-> "NH2" Residue "A ARG 2045": "NH1" <-> "NH2" Residue "A GLU 2085": "OE1" <-> "OE2" Residue "A ARG 2122": "NH1" <-> "NH2" Residue "A GLU 2230": "OE1" <-> "OE2" Residue "A GLU 2311": "OE1" <-> "OE2" Residue "A ARG 2312": "NH1" <-> "NH2" Residue "A GLU 2403": "OE1" <-> "OE2" Residue "A ARG 2413": "NH1" <-> "NH2" Residue "A ARG 2443": "NH1" <-> "NH2" Residue "A ARG 2477": "NH1" <-> "NH2" Residue "A GLU 2488": "OE1" <-> "OE2" Residue "A GLU 2503": "OE1" <-> "OE2" Residue "A GLU 2508": "OE1" <-> "OE2" Residue "A GLU 2516": "OE1" <-> "OE2" Residue "A GLU 2527": "OE1" <-> "OE2" Residue "B GLU 601": "OE1" <-> "OE2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B ARG 715": "NH1" <-> "NH2" Residue "B ARG 793": "NH1" <-> "NH2" Residue "B ARG 841": "NH1" <-> "NH2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ARG 1067": "NH1" <-> "NH2" Residue "B GLU 1100": "OE1" <-> "OE2" Residue "B ARG 1127": "NH1" <-> "NH2" Residue "B GLU 1146": "OE1" <-> "OE2" Residue "B ARG 1161": "NH1" <-> "NH2" Residue "B GLU 1190": "OE1" <-> "OE2" Residue "B ARG 1199": "NH1" <-> "NH2" Residue "B ARG 1223": "NH1" <-> "NH2" Residue "B ARG 1246": "NH1" <-> "NH2" Residue "B GLU 1263": "OE1" <-> "OE2" Residue "B ARG 1282": "NH1" <-> "NH2" Residue "B GLU 1301": "OE1" <-> "OE2" Residue "B ARG 1325": "NH1" <-> "NH2" Residue "B ARG 1381": "NH1" <-> "NH2" Residue "B ARG 1386": "NH1" <-> "NH2" Residue "B ARG 1412": "NH1" <-> "NH2" Residue "B GLU 1427": "OE1" <-> "OE2" Residue "B ARG 1441": "NH1" <-> "NH2" Residue "B ARG 1483": "NH1" <-> "NH2" Residue "B GLU 1507": "OE1" <-> "OE2" Residue "B GLU 1531": "OE1" <-> "OE2" Residue "B GLU 1537": "OE1" <-> "OE2" Residue "B ARG 1538": "NH1" <-> "NH2" Residue "B ARG 1550": "NH1" <-> "NH2" Residue "B ARG 1558": "NH1" <-> "NH2" Residue "B GLU 1566": "OE1" <-> "OE2" Residue "B GLU 1578": "OE1" <-> "OE2" Residue "B ARG 1629": "NH1" <-> "NH2" Residue "B GLU 1654": "OE1" <-> "OE2" Residue "B ARG 1677": "NH1" <-> "NH2" Residue "B GLU 1689": "OE1" <-> "OE2" Residue "B ARG 1711": "NH1" <-> "NH2" Residue "B ARG 1731": "NH1" <-> "NH2" Residue "B GLU 1760": "OE1" <-> "OE2" Residue "B GLU 1790": "OE1" <-> "OE2" Residue "B GLU 1797": "OE1" <-> "OE2" Residue "B GLU 1805": "OE1" <-> "OE2" Residue "B ARG 1847": "NH1" <-> "NH2" Residue "B GLU 1874": "OE1" <-> "OE2" Residue "B GLU 1876": "OE1" <-> "OE2" Residue "B GLU 1878": "OE1" <-> "OE2" Residue "B PHE 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1901": "OE1" <-> "OE2" Residue "B ARG 1915": "NH1" <-> "NH2" Residue "B ARG 1918": "NH1" <-> "NH2" Residue "B ARG 1943": "NH1" <-> "NH2" Residue "B ARG 1957": "NH1" <-> "NH2" Residue "B ARG 1968": "NH1" <-> "NH2" Residue "B ARG 1973": "NH1" <-> "NH2" Residue "B ARG 1983": "NH1" <-> "NH2" Residue "B ARG 2026": "NH1" <-> "NH2" Residue "B ARG 2039": "NH1" <-> "NH2" Residue "B ARG 2045": "NH1" <-> "NH2" Residue "B GLU 2085": "OE1" <-> "OE2" Residue "B ARG 2122": "NH1" <-> "NH2" Residue "B GLU 2230": "OE1" <-> "OE2" Residue "B GLU 2311": "OE1" <-> "OE2" Residue "B ARG 2312": "NH1" <-> "NH2" Residue "B GLU 2403": "OE1" <-> "OE2" Residue "B ARG 2413": "NH1" <-> "NH2" Residue "B ARG 2443": "NH1" <-> "NH2" Residue "B ARG 2477": "NH1" <-> "NH2" Residue "B GLU 2488": "OE1" <-> "OE2" Residue "B GLU 2503": "OE1" <-> "OE2" Residue "B GLU 2508": "OE1" <-> "OE2" Residue "B GLU 2516": "OE1" <-> "OE2" Residue "B GLU 2527": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28245 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 14057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1795, 14057 Classifications: {'peptide': 1795} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1718} Chain breaks: 8 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 17, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 18, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 165 Chain: "B" Number of atoms: 14070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1795, 14070 Classifications: {'peptide': 1795} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1718} Chain breaks: 8 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 17, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 152 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'ATP': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'ATP': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.80, per 1000 atoms: 0.52 Number of scatterers: 28245 At special positions: 0 Unit cell: (175.938, 124.726, 147.028, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 178 16.00 P 10 15.00 O 5147 8.00 N 4873 7.00 C 18037 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: 10.96 Conformation dependent library (CDL) restraints added in 4.8 seconds 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 40 sheets defined 33.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.779A pdb=" N SER A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 596 removed outlier: 4.189A pdb=" N LEU A 593 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 605 Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.819A pdb=" N ILE A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 611 " --> pdb=" O LEU A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 611' Processing helix chain 'A' and resid 625 through 638 removed outlier: 3.811A pdb=" N SER A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 657 Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 662 through 667 Processing helix chain 'A' and resid 670 through 679 removed outlier: 4.256A pdb=" N HIS A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 removed outlier: 3.782A pdb=" N LYS A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 715 removed outlier: 3.692A pdb=" N ASN A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 714 " --> pdb=" O ASN A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 731 removed outlier: 3.691A pdb=" N LEU A 729 " --> pdb=" O VAL A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.524A pdb=" N GLU A 750 " --> pdb=" O CYS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.873A pdb=" N LEU A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 761 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 removed outlier: 3.710A pdb=" N LYS A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 776 " --> pdb=" O ARG A 772 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 795 removed outlier: 3.646A pdb=" N ARG A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.720A pdb=" N LEU A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 833 through 853 removed outlier: 3.695A pdb=" N GLU A 853 " --> pdb=" O LYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1009 through 1013 Processing helix chain 'A' and resid 1029 through 1033 Processing helix chain 'A' and resid 1053 through 1057 Processing helix chain 'A' and resid 1101 through 1106 Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.728A pdb=" N ASN A1194 " --> pdb=" O GLU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 4.066A pdb=" N TRP A1217 " --> pdb=" O PRO A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1245 Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.548A pdb=" N GLY A1265 " --> pdb=" O PRO A1262 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1267 " --> pdb=" O ILE A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1291 removed outlier: 3.653A pdb=" N GLY A1289 " --> pdb=" O ASN A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1328 removed outlier: 3.852A pdb=" N LEU A1326 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A1327 " --> pdb=" O GLN A1323 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A1328 " --> pdb=" O GLN A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1355 Processing helix chain 'A' and resid 1404 through 1408 Processing helix chain 'A' and resid 1420 through 1424 Processing helix chain 'A' and resid 1428 through 1430 No H-bonds generated for 'chain 'A' and resid 1428 through 1430' Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1463 through 1465 No H-bonds generated for 'chain 'A' and resid 1463 through 1465' Processing helix chain 'A' and resid 1466 through 1473 Processing helix chain 'A' and resid 1494 through 1509 removed outlier: 3.921A pdb=" N LEU A1500 " --> pdb=" O ALA A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1520 Processing helix chain 'A' and resid 1525 through 1539 removed outlier: 4.042A pdb=" N LYS A1539 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1560 removed outlier: 3.545A pdb=" N VAL A1557 " --> pdb=" O LEU A1553 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A1558 " --> pdb=" O LEU A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1579 removed outlier: 3.920A pdb=" N HIS A1574 " --> pdb=" O PRO A1570 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A1579 " --> pdb=" O PHE A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1607 removed outlier: 4.144A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A1605 " --> pdb=" O LYS A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1654 removed outlier: 3.783A pdb=" N PHE A1650 " --> pdb=" O MET A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1709 Processing helix chain 'A' and resid 1770 through 1792 removed outlier: 3.575A pdb=" N ILE A1775 " --> pdb=" O ARG A1771 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A1776 " --> pdb=" O LYS A1772 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP A1782 " --> pdb=" O GLY A1778 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A1783 " --> pdb=" O GLN A1779 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A1788 " --> pdb=" O ILE A1784 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A1790 " --> pdb=" O SER A1786 " (cutoff:3.500A) Processing helix chain 'A' and resid 1829 through 1834 Processing helix chain 'A' and resid 1852 through 1856 Processing helix chain 'A' and resid 1865 through 1869 removed outlier: 3.640A pdb=" N MET A1869 " --> pdb=" O ARG A1866 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1925 removed outlier: 3.834A pdb=" N VAL A1922 " --> pdb=" O ARG A1918 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL A1923 " --> pdb=" O GLN A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 removed outlier: 3.763A pdb=" N LEU A1958 " --> pdb=" O SER A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1986 removed outlier: 3.640A pdb=" N ARG A1973 " --> pdb=" O THR A1969 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A1975 " --> pdb=" O GLN A1971 " (cutoff:3.500A) Processing helix chain 'A' and resid 2017 through 2026 removed outlier: 3.887A pdb=" N ALA A2021 " --> pdb=" O ASP A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2051 through 2068 removed outlier: 4.249A pdb=" N ASP A2055 " --> pdb=" O ASN A2051 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A2056 " --> pdb=" O GLN A2052 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR A2057 " --> pdb=" O GLN A2053 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2077 removed outlier: 3.866A pdb=" N VAL A2074 " --> pdb=" O GLY A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2089 removed outlier: 3.540A pdb=" N GLU A2085 " --> pdb=" O ASN A2081 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A2086 " --> pdb=" O GLU A2082 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU A2087 " --> pdb=" O PHE A2083 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A2089 " --> pdb=" O GLU A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2115 Processing helix chain 'A' and resid 2118 through 2122 Processing helix chain 'A' and resid 2124 through 2131 Processing helix chain 'A' and resid 2278 through 2282 removed outlier: 4.142A pdb=" N LYS A2281 " --> pdb=" O LYS A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2389 through 2397 removed outlier: 4.910A pdb=" N GLU A2395 " --> pdb=" O HIS A2391 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A2396 " --> pdb=" O PHE A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2402 through 2407 removed outlier: 3.551A pdb=" N LYS A2405 " --> pdb=" O LYS A2402 " (cutoff:3.500A) Processing helix chain 'A' and resid 2481 through 2485 Processing helix chain 'A' and resid 2499 through 2527 removed outlier: 3.745A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A2508 " --> pdb=" O VAL A2504 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A2512 " --> pdb=" O GLU A2508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A2514 " --> pdb=" O HIS A2510 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A2522 " --> pdb=" O ALA A2518 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A2524 " --> pdb=" O LYS A2520 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER A2525 " --> pdb=" O MET A2521 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A2526 " --> pdb=" O ARG A2522 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.779A pdb=" N SER B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 596 removed outlier: 4.190A pdb=" N LEU B 593 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 605 Processing helix chain 'B' and resid 606 through 611 removed outlier: 3.820A pdb=" N ILE B 610 " --> pdb=" O GLY B 606 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY B 611 " --> pdb=" O LEU B 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 606 through 611' Processing helix chain 'B' and resid 625 through 638 removed outlier: 3.812A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 657 Processing helix chain 'B' and resid 659 through 661 No H-bonds generated for 'chain 'B' and resid 659 through 661' Processing helix chain 'B' and resid 662 through 667 Processing helix chain 'B' and resid 670 through 679 removed outlier: 4.256A pdb=" N HIS B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 703 removed outlier: 3.782A pdb=" N LYS B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 715 removed outlier: 3.692A pdb=" N ASN B 710 " --> pdb=" O ASP B 706 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 714 " --> pdb=" O ASN B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 731 removed outlier: 3.690A pdb=" N LEU B 729 " --> pdb=" O VAL B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.524A pdb=" N GLU B 750 " --> pdb=" O CYS B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 763 removed outlier: 3.873A pdb=" N LEU B 760 " --> pdb=" O LYS B 756 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 761 " --> pdb=" O LEU B 757 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 781 removed outlier: 3.710A pdb=" N LYS B 773 " --> pdb=" O GLN B 769 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 776 " --> pdb=" O ARG B 772 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 795 removed outlier: 3.646A pdb=" N ARG B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 819 removed outlier: 3.720A pdb=" N LEU B 818 " --> pdb=" O GLU B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 833 through 853 removed outlier: 3.695A pdb=" N GLU B 853 " --> pdb=" O LYS B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1001 Processing helix chain 'B' and resid 1009 through 1013 Processing helix chain 'B' and resid 1029 through 1033 Processing helix chain 'B' and resid 1053 through 1057 Processing helix chain 'B' and resid 1101 through 1106 Processing helix chain 'B' and resid 1189 through 1194 removed outlier: 3.728A pdb=" N ASN B1194 " --> pdb=" O GLU B1190 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1217 removed outlier: 4.066A pdb=" N TRP B1217 " --> pdb=" O PRO B1214 " (cutoff:3.500A) Processing helix chain 'B' and resid 1241 through 1245 Processing helix chain 'B' and resid 1261 through 1267 removed outlier: 3.548A pdb=" N GLY B1265 " --> pdb=" O PRO B1262 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B1267 " --> pdb=" O ILE B1264 " (cutoff:3.500A) Processing helix chain 'B' and resid 1285 through 1291 removed outlier: 3.653A pdb=" N GLY B1289 " --> pdb=" O ASN B1286 " (cutoff:3.500A) Processing helix chain 'B' and resid 1316 through 1328 removed outlier: 3.852A pdb=" N LEU B1326 " --> pdb=" O LEU B1322 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS B1327 " --> pdb=" O GLN B1323 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B1328 " --> pdb=" O GLN B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1350 through 1355 Processing helix chain 'B' and resid 1404 through 1408 Processing helix chain 'B' and resid 1420 through 1424 Processing helix chain 'B' and resid 1428 through 1430 No H-bonds generated for 'chain 'B' and resid 1428 through 1430' Processing helix chain 'B' and resid 1431 through 1442 Processing helix chain 'B' and resid 1463 through 1465 No H-bonds generated for 'chain 'B' and resid 1463 through 1465' Processing helix chain 'B' and resid 1466 through 1473 Processing helix chain 'B' and resid 1494 through 1509 removed outlier: 3.921A pdb=" N LEU B1500 " --> pdb=" O ALA B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1517 through 1520 Processing helix chain 'B' and resid 1525 through 1539 removed outlier: 4.042A pdb=" N LYS B1539 " --> pdb=" O LEU B1535 " (cutoff:3.500A) Processing helix chain 'B' and resid 1550 through 1560 removed outlier: 3.545A pdb=" N VAL B1557 " --> pdb=" O LEU B1553 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG B1558 " --> pdb=" O LEU B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1568 through 1579 removed outlier: 3.920A pdb=" N HIS B1574 " --> pdb=" O PRO B1570 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B1579 " --> pdb=" O PHE B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1599 through 1607 removed outlier: 4.145A pdb=" N LEU B1603 " --> pdb=" O GLU B1599 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B1605 " --> pdb=" O LYS B1601 " (cutoff:3.500A) Processing helix chain 'B' and resid 1644 through 1654 removed outlier: 3.784A pdb=" N PHE B1650 " --> pdb=" O MET B1646 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1709 Processing helix chain 'B' and resid 1770 through 1792 removed outlier: 3.575A pdb=" N ILE B1775 " --> pdb=" O ARG B1771 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B1776 " --> pdb=" O LYS B1772 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP B1782 " --> pdb=" O GLY B1778 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS B1783 " --> pdb=" O GLN B1779 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B1788 " --> pdb=" O ILE B1784 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B1790 " --> pdb=" O SER B1786 " (cutoff:3.500A) Processing helix chain 'B' and resid 1829 through 1834 Processing helix chain 'B' and resid 1852 through 1856 Processing helix chain 'B' and resid 1865 through 1869 removed outlier: 3.641A pdb=" N MET B1869 " --> pdb=" O ARG B1866 " (cutoff:3.500A) Processing helix chain 'B' and resid 1913 through 1925 removed outlier: 3.834A pdb=" N VAL B1922 " --> pdb=" O ARG B1918 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B1923 " --> pdb=" O GLN B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1962 removed outlier: 3.763A pdb=" N LEU B1958 " --> pdb=" O SER B1954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1969 through 1986 removed outlier: 3.640A pdb=" N ARG B1973 " --> pdb=" O THR B1969 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B1975 " --> pdb=" O GLN B1971 " (cutoff:3.500A) Processing helix chain 'B' and resid 2017 through 2026 removed outlier: 3.887A pdb=" N ALA B2021 " --> pdb=" O ASP B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2040 through 2045 Processing helix chain 'B' and resid 2051 through 2068 removed outlier: 4.249A pdb=" N ASP B2055 " --> pdb=" O ASN B2051 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B2056 " --> pdb=" O GLN B2052 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B2057 " --> pdb=" O GLN B2053 " (cutoff:3.500A) Processing helix chain 'B' and resid 2070 through 2077 removed outlier: 3.866A pdb=" N VAL B2074 " --> pdb=" O GLY B2070 " (cutoff:3.500A) Processing helix chain 'B' and resid 2079 through 2089 removed outlier: 3.541A pdb=" N GLU B2085 " --> pdb=" O ASN B2081 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B2086 " --> pdb=" O GLU B2082 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU B2087 " --> pdb=" O PHE B2083 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B2089 " --> pdb=" O GLU B2085 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2099 removed outlier: 3.659A pdb=" N TYR B2099 " --> pdb=" O PRO B2095 " (cutoff:3.500A) Processing helix chain 'B' and resid 2107 through 2115 Processing helix chain 'B' and resid 2118 through 2122 Processing helix chain 'B' and resid 2124 through 2131 Processing helix chain 'B' and resid 2278 through 2282 removed outlier: 4.141A pdb=" N LYS B2281 " --> pdb=" O LYS B2278 " (cutoff:3.500A) Processing helix chain 'B' and resid 2389 through 2397 removed outlier: 4.910A pdb=" N GLU B2395 " --> pdb=" O HIS B2391 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B2396 " --> pdb=" O PHE B2392 " (cutoff:3.500A) Processing helix chain 'B' and resid 2402 through 2407 removed outlier: 3.552A pdb=" N LYS B2405 " --> pdb=" O LYS B2402 " (cutoff:3.500A) Processing helix chain 'B' and resid 2481 through 2485 Processing helix chain 'B' and resid 2499 through 2527 removed outlier: 3.746A pdb=" N GLN B2505 " --> pdb=" O PRO B2501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B2508 " --> pdb=" O VAL B2504 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B2512 " --> pdb=" O GLU B2508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B2514 " --> pdb=" O HIS B2510 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B2522 " --> pdb=" O ALA B2518 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B2524 " --> pdb=" O LYS B2520 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER B2525 " --> pdb=" O MET B2521 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B2526 " --> pdb=" O ARG B2522 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 802 through 804 removed outlier: 6.481A pdb=" N ILE A 803 " --> pdb=" O ASP A 988 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU A 987 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A1016 " --> pdb=" O ASP A1041 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 6.972A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A1113 " --> pdb=" O PHE A1088 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1177 through 1179 removed outlier: 7.017A pdb=" N LEU A1178 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A1201 " --> pdb=" O LEU A1226 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU A1250 " --> pdb=" O ASP A1274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1329 through 1332 removed outlier: 4.286A pdb=" N GLN A1521 " --> pdb=" O TYR A1332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1336 through 1339 removed outlier: 3.665A pdb=" N LEU A1388 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A1390 " --> pdb=" O TRP A1376 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A1376 " --> pdb=" O LEU A1390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1415 through 1418 removed outlier: 7.340A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL A1447 " --> pdb=" O ARG A1483 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR A1485 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A1449 " --> pdb=" O TYR A1485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1547 through 1549 Processing sheet with id=AA8, first strand: chain 'A' and resid 1680 through 1681 removed outlier: 3.590A pdb=" N ARG B1731 " --> pdb=" O GLU A1681 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1690 through 1692 removed outlier: 6.456A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS A1748 " --> pdb=" O ASN A1741 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN A1741 " --> pdb=" O CYS A1748 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1731 through 1732 removed outlier: 3.586A pdb=" N ARG A1731 " --> pdb=" O GLU B1681 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1811 through 1814 Processing sheet with id=AB3, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AB4, first strand: chain 'A' and resid 1896 through 1898 removed outlier: 3.554A pdb=" N GLY A1939 " --> pdb=" O MET A1944 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A1937 " --> pdb=" O VAL A1946 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2144 through 2145 removed outlier: 3.501A pdb=" N LEU A2493 " --> pdb=" O ILE A2144 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A2467 " --> pdb=" O LEU A2463 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU A2463 " --> pdb=" O LYS A2467 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2155 through 2157 Processing sheet with id=AB7, first strand: chain 'A' and resid 2178 through 2179 Processing sheet with id=AB8, first strand: chain 'A' and resid 2199 through 2207 removed outlier: 6.870A pdb=" N GLY A2218 " --> pdb=" O LEU A2200 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A2202 " --> pdb=" O VAL A2216 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A2216 " --> pdb=" O LEU A2202 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU A2204 " --> pdb=" O TRP A2214 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TRP A2214 " --> pdb=" O LEU A2204 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N HIS A2206 " --> pdb=" O GLU A2212 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLU A2212 " --> pdb=" O HIS A2206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A2226 " --> pdb=" O HIS A2236 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A2236 " --> pdb=" O VAL A2226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2264 through 2265 removed outlier: 3.574A pdb=" N ALA A2273 " --> pdb=" O VAL A2265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A2272 " --> pdb=" O LEU A2291 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.636A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2414 through 2419 removed outlier: 3.581A pdb=" N THR A2416 " --> pdb=" O GLY A2428 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A2434 " --> pdb=" O VAL A2447 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL A2447 " --> pdb=" O ILE A2434 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU A2436 " --> pdb=" O ILE A2445 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2477 through 2478 removed outlier: 3.677A pdb=" N GLU A2488 " --> pdb=" O LYS A2478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 802 through 804 removed outlier: 6.482A pdb=" N ILE B 803 " --> pdb=" O ASP B 988 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 987 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B1016 " --> pdb=" O ASP B1041 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 1063 through 1064 removed outlier: 6.972A pdb=" N LEU B1063 " --> pdb=" O ASN B1089 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B1113 " --> pdb=" O PHE B1088 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1177 through 1179 removed outlier: 7.017A pdb=" N LEU B1178 " --> pdb=" O ASP B1202 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B1201 " --> pdb=" O LEU B1226 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B1250 " --> pdb=" O ASP B1274 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1329 through 1332 removed outlier: 4.286A pdb=" N GLN B1521 " --> pdb=" O TYR B1332 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1336 through 1339 removed outlier: 3.666A pdb=" N LEU B1388 " --> pdb=" O ILE B1378 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B1390 " --> pdb=" O TRP B1376 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP B1376 " --> pdb=" O LEU B1390 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1415 through 1418 removed outlier: 7.340A pdb=" N TYR B1415 " --> pdb=" O ILE B1448 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL B1450 " --> pdb=" O TYR B1415 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA B1417 " --> pdb=" O VAL B1450 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B1447 " --> pdb=" O ARG B1483 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B1485 " --> pdb=" O VAL B1447 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B1449 " --> pdb=" O TYR B1485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 1547 through 1549 Processing sheet with id=AD2, first strand: chain 'B' and resid 1690 through 1692 removed outlier: 6.456A pdb=" N TYR B1747 " --> pdb=" O PRO B1768 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS B1748 " --> pdb=" O ASN B1741 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN B1741 " --> pdb=" O CYS B1748 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1811 through 1814 Processing sheet with id=AD4, first strand: chain 'B' and resid 1840 through 1841 Processing sheet with id=AD5, first strand: chain 'B' and resid 1896 through 1898 removed outlier: 3.555A pdb=" N GLY B1939 " --> pdb=" O MET B1944 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B1937 " --> pdb=" O VAL B1946 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU B1948 " --> pdb=" O LEU B1935 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU B1935 " --> pdb=" O GLU B1948 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 2144 through 2145 removed outlier: 3.502A pdb=" N LEU B2493 " --> pdb=" O ILE B2144 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B2467 " --> pdb=" O LEU B2463 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU B2463 " --> pdb=" O LYS B2467 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 2155 through 2157 Processing sheet with id=AD8, first strand: chain 'B' and resid 2178 through 2179 Processing sheet with id=AD9, first strand: chain 'B' and resid 2199 through 2207 removed outlier: 6.870A pdb=" N GLY B2218 " --> pdb=" O LEU B2200 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU B2202 " --> pdb=" O VAL B2216 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B2216 " --> pdb=" O LEU B2202 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU B2204 " --> pdb=" O TRP B2214 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TRP B2214 " --> pdb=" O LEU B2204 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N HIS B2206 " --> pdb=" O GLU B2212 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLU B2212 " --> pdb=" O HIS B2206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B2226 " --> pdb=" O HIS B2236 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B2236 " --> pdb=" O VAL B2226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 2264 through 2265 removed outlier: 3.574A pdb=" N ALA B2273 " --> pdb=" O VAL B2265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B2272 " --> pdb=" O LEU B2291 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 2354 through 2359 removed outlier: 6.636A pdb=" N ALA B2366 " --> pdb=" O ILE B2355 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL B2357 " --> pdb=" O TYR B2364 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR B2364 " --> pdb=" O VAL B2357 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS B2367 " --> pdb=" O VAL B2372 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B2372 " --> pdb=" O LYS B2367 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 2414 through 2419 removed outlier: 3.582A pdb=" N THR B2416 " --> pdb=" O GLY B2428 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B2434 " --> pdb=" O VAL B2447 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL B2447 " --> pdb=" O ILE B2434 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU B2436 " --> pdb=" O ILE B2445 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 2477 through 2478 removed outlier: 3.676A pdb=" N GLU B2488 " --> pdb=" O LYS B2478 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 1905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.11 Time building geometry restraints manager: 11.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5441 1.33 - 1.45: 6315 1.45 - 1.57: 16750 1.57 - 1.69: 16 1.69 - 1.81: 260 Bond restraints: 28782 Sorted by residual: bond pdb=" C4 ATP B2602 " pdb=" C5 ATP B2602 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C5 ATP B2602 " pdb=" C6 ATP B2602 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.41e+01 bond pdb=" C4 ATP A2602 " pdb=" N9 ATP A2602 " ideal model delta sigma weight residual 1.374 1.309 0.065 1.00e-02 1.00e+04 4.19e+01 bond pdb=" C5 ATP A2602 " pdb=" N7 ATP A2602 " ideal model delta sigma weight residual 1.387 1.323 0.064 1.00e-02 1.00e+04 4.15e+01 bond pdb=" C4 ATP A2602 " pdb=" C5 ATP A2602 " ideal model delta sigma weight residual 1.388 1.443 -0.055 1.00e-02 1.00e+04 3.07e+01 ... (remaining 28777 not shown) Histogram of bond angle deviations from ideal: 97.50 - 105.22: 587 105.22 - 112.94: 16102 112.94 - 120.66: 12336 120.66 - 128.38: 9721 128.38 - 136.10: 222 Bond angle restraints: 38968 Sorted by residual: angle pdb=" PB ATP B2602 " pdb=" O3B ATP B2602 " pdb=" PG ATP B2602 " ideal model delta sigma weight residual 139.87 121.27 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PA ATP B2602 " pdb=" O3A ATP B2602 " pdb=" PB ATP B2602 " ideal model delta sigma weight residual 136.83 120.34 16.49 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP A2602 " pdb=" O3A ATP A2602 " pdb=" PB ATP A2602 " ideal model delta sigma weight residual 136.83 121.34 15.49 1.00e+00 1.00e+00 2.40e+02 angle pdb=" PB ATP A2602 " pdb=" O3B ATP A2602 " pdb=" PG ATP A2602 " ideal model delta sigma weight residual 139.87 127.62 12.25 1.00e+00 1.00e+00 1.50e+02 angle pdb=" C5 ATP B2602 " pdb=" C4 ATP B2602 " pdb=" N3 ATP B2602 " ideal model delta sigma weight residual 126.80 118.93 7.87 1.00e+00 1.00e+00 6.19e+01 ... (remaining 38963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.62: 16160 20.62 - 41.25: 1304 41.25 - 61.87: 130 61.87 - 82.49: 33 82.49 - 103.11: 9 Dihedral angle restraints: 17636 sinusoidal: 7138 harmonic: 10498 Sorted by residual: dihedral pdb=" CA ARG A1941 " pdb=" C ARG A1941 " pdb=" N PRO A1942 " pdb=" CA PRO A1942 " ideal model delta harmonic sigma weight residual 0.00 -34.90 34.90 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" C LEU A2137 " pdb=" N LEU A2137 " pdb=" CA LEU A2137 " pdb=" CB LEU A2137 " ideal model delta harmonic sigma weight residual -122.60 -107.90 -14.70 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" C LEU B2137 " pdb=" N LEU B2137 " pdb=" CA LEU B2137 " pdb=" CB LEU B2137 " ideal model delta harmonic sigma weight residual -122.60 -108.35 -14.25 0 2.50e+00 1.60e-01 3.25e+01 ... (remaining 17633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3972 0.070 - 0.139: 513 0.139 - 0.209: 46 0.209 - 0.278: 9 0.278 - 0.348: 4 Chirality restraints: 4544 Sorted by residual: chirality pdb=" CA LEU A2137 " pdb=" N LEU A2137 " pdb=" C LEU A2137 " pdb=" CB LEU A2137 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA LEU B2137 " pdb=" N LEU B2137 " pdb=" C LEU B2137 " pdb=" CB LEU B2137 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA VAL B1598 " pdb=" N VAL B1598 " pdb=" C VAL B1598 " pdb=" CB VAL B1598 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 4541 not shown) Planarity restraints: 4891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP B2496 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C TRP B2496 " -0.070 2.00e-02 2.50e+03 pdb=" O TRP B2496 " 0.027 2.00e-02 2.50e+03 pdb=" N ASP B2497 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A2496 " -0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C TRP A2496 " 0.070 2.00e-02 2.50e+03 pdb=" O TRP A2496 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP A2497 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B1057 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C MET B1057 " -0.037 2.00e-02 2.50e+03 pdb=" O MET B1057 " 0.014 2.00e-02 2.50e+03 pdb=" N SER B1058 " 0.012 2.00e-02 2.50e+03 ... (remaining 4888 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 651 2.68 - 3.23: 28565 3.23 - 3.79: 39794 3.79 - 4.34: 57836 4.34 - 4.90: 92969 Nonbonded interactions: 219815 Sorted by model distance: nonbonded pdb=" OH TYR A1992 " pdb=" O ALA A2016 " model vdw 2.121 2.440 nonbonded pdb=" OH TYR B1992 " pdb=" O ALA B2016 " model vdw 2.121 2.440 nonbonded pdb=" O SER A2213 " pdb=" OG1 THR A2229 " model vdw 2.161 2.440 nonbonded pdb=" O SER B2213 " pdb=" OG1 THR B2229 " model vdw 2.161 2.440 nonbonded pdb=" NH1 ARG A1731 " pdb=" OE2 GLU B1681 " model vdw 2.181 2.520 ... (remaining 219810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 558 through 1424 or (resid 1425 through 1426 and (name N o \ r name CA or name C or name O or name CB )) or resid 1427 through 2527 or resid \ 2601 through 2602)) selection = (chain 'B' and (resid 558 through 1680 or (resid 1681 and (name N or name CA or \ name C or name O or name CB )) or resid 1682 through 1683 or (resid 1684 and (na \ me N or name CA or name C or name O or name CB )) or resid 1685 through 1688 or \ (resid 1689 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 90 through 1744 or (resid 1745 through 1746 and (name N or name CA or name C or \ name O or name CB )) or resid 1747 through 2527 or resid 2601 through 2602)) } 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: 5.940 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: 23.750 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 75.430 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.130 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 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 0.077 28782 Z= 0.304 Angle : 0.808 18.595 38968 Z= 0.485 Chirality : 0.049 0.348 4544 Planarity : 0.004 0.043 4891 Dihedral : 14.564 103.113 10800 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 0.06 % Allowed : 8.38 % Favored : 91.55 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -5.40 (0.11), residues: 3554 helix: -4.02 (0.10), residues: 982 sheet: -3.78 (0.20), residues: 464 loop : -3.45 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1705 HIS 0.011 0.001 HIS A1310 PHE 0.014 0.001 PHE A1585 TYR 0.014 0.002 TYR A2364 ARG 0.007 0.000 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 461 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 MET cc_start: 0.3474 (ttt) cc_final: 0.3143 (ttp) REVERT: A 800 ASN cc_start: 0.6675 (t0) cc_final: 0.6467 (t0) REVERT: A 1431 MET cc_start: 0.7897 (tmm) cc_final: 0.7694 (ttm) REVERT: A 1516 GLN cc_start: 0.7306 (mm110) cc_final: 0.6963 (tm-30) REVERT: A 1754 VAL cc_start: 0.8313 (p) cc_final: 0.7885 (m) REVERT: B 586 MET cc_start: 0.3320 (ttt) cc_final: 0.2980 (ttp) REVERT: B 800 ASN cc_start: 0.6672 (t0) cc_final: 0.6449 (t0) REVERT: B 1516 GLN cc_start: 0.7300 (mm110) cc_final: 0.6981 (tt0) REVERT: B 1788 MET cc_start: 0.8768 (tpp) cc_final: 0.8263 (tpp) outliers start: 2 outliers final: 0 residues processed: 463 average time/residue: 0.4341 time to fit residues: 307.7156 Evaluate side-chains 213 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.166 ------------------------------------------------------------------------------- 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: 0.7980 chunk 271 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 chunk 280 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 325 optimal weight: 30.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 ASN A 992 ASN ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN A1140 HIS A1163 ASN A1516 GLN ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1871 ASN A1998 HIS A2053 GLN ** A2313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2433 HIS B 682 ASN B 992 ASN B1020 GLN ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN B1163 ASN B1305 ASN B1516 GLN ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1871 ASN B2053 GLN ** B2313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2433 HIS B2476 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28782 Z= 0.265 Angle : 0.693 10.703 38968 Z= 0.349 Chirality : 0.045 0.168 4544 Planarity : 0.004 0.045 4891 Dihedral : 6.771 83.363 3910 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 2.05 % Allowed : 16.13 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.34 (0.12), residues: 3554 helix: -2.54 (0.13), residues: 1088 sheet: -3.33 (0.22), residues: 456 loop : -3.05 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A2496 HIS 0.007 0.001 HIS B 669 PHE 0.015 0.002 PHE B 691 TYR 0.020 0.002 TYR B1739 ARG 0.005 0.001 ARG A2026 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 235 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1702 MET cc_start: 0.8458 (tpp) cc_final: 0.8230 (tpp) REVERT: B 1702 MET cc_start: 0.8495 (tpp) cc_final: 0.8227 (tpp) outliers start: 64 outliers final: 40 residues processed: 285 average time/residue: 0.3768 time to fit residues: 176.4515 Evaluate side-chains 218 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 1049 SER Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1650 PHE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2118 ASN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2426 TRP Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1268 GLU Chi-restraints excluded: chain B residue 1650 PHE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1850 ILE Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2118 ASN Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2426 TRP Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 0.0770 chunk 100 optimal weight: 0.6980 chunk 270 optimal weight: 0.0170 chunk 221 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 325 optimal weight: 30.0000 chunk 351 optimal weight: 8.9990 chunk 290 optimal weight: 0.8980 chunk 322 optimal weight: 10.0000 chunk 111 optimal weight: 0.3980 chunk 261 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 ASN A1303 HIS A1516 GLN ** A2313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2453 ASN ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 ASN B1303 HIS B1758 HIS ** B2313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2453 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28782 Z= 0.156 Angle : 0.589 10.317 38968 Z= 0.295 Chirality : 0.042 0.147 4544 Planarity : 0.004 0.046 4891 Dihedral : 6.293 73.142 3910 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.37 % Allowed : 16.77 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.74 (0.13), residues: 3554 helix: -1.89 (0.14), residues: 1112 sheet: -3.06 (0.21), residues: 492 loop : -2.73 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2168 HIS 0.005 0.001 HIS B2510 PHE 0.020 0.001 PHE B2079 TYR 0.017 0.001 TYR B1739 ARG 0.004 0.000 ARG B1127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 199 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1754 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8095 (m) REVERT: B 1754 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8082 (m) outliers start: 74 outliers final: 45 residues processed: 264 average time/residue: 0.3727 time to fit residues: 163.5238 Evaluate side-chains 230 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 183 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 1240 LYS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1650 PHE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2426 TRP Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1650 PHE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1799 ASP Chi-restraints excluded: chain B residue 1850 ILE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Chi-restraints excluded: chain B residue 2469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 218 optimal weight: 0.2980 chunk 326 optimal weight: 20.0000 chunk 346 optimal weight: 0.0970 chunk 170 optimal weight: 3.9990 chunk 309 optimal weight: 0.0570 chunk 93 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28782 Z= 0.146 Angle : 0.568 10.390 38968 Z= 0.282 Chirality : 0.042 0.164 4544 Planarity : 0.004 0.046 4891 Dihedral : 6.050 79.239 3910 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.04 % Allowed : 17.12 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.32 (0.13), residues: 3554 helix: -1.40 (0.15), residues: 1124 sheet: -2.87 (0.22), residues: 524 loop : -2.54 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A2376 HIS 0.004 0.001 HIS B2173 PHE 0.012 0.001 PHE A1650 TYR 0.014 0.001 TYR B1739 ARG 0.004 0.000 ARG B1866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 209 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1364 MET cc_start: -0.0152 (tpt) cc_final: -0.0622 (tpt) REVERT: A 1390 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8091 (pp) REVERT: A 1754 VAL cc_start: 0.8404 (p) cc_final: 0.8087 (m) REVERT: B 1364 MET cc_start: -0.0136 (tpt) cc_final: -0.0585 (tpt) REVERT: B 1390 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8163 (pp) outliers start: 95 outliers final: 47 residues processed: 291 average time/residue: 0.3657 time to fit residues: 178.8914 Evaluate side-chains 232 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 183 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 1049 SER Chi-restraints excluded: chain A residue 1240 LYS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2426 TRP Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2469 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1268 GLU Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1394 ASP Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1799 ASP Chi-restraints excluded: chain B residue 1850 ILE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 2027 MET Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 5.9990 chunk 196 optimal weight: 0.0270 chunk 5 optimal weight: 8.9990 chunk 257 optimal weight: 0.1980 chunk 142 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 176 optimal weight: 1.9990 chunk 310 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 overall best weight: 2.2444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1183 ASN A1254 HIS A1353 GLN A1407 HIS ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS B1353 GLN B1407 HIS ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 28782 Z= 0.360 Angle : 0.694 11.223 38968 Z= 0.345 Chirality : 0.046 0.166 4544 Planarity : 0.004 0.046 4891 Dihedral : 6.393 84.740 3910 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 3.94 % Allowed : 17.09 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.27 (0.13), residues: 3554 helix: -1.24 (0.15), residues: 1104 sheet: -2.90 (0.22), residues: 488 loop : -2.59 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A2376 HIS 0.005 0.001 HIS A1574 PHE 0.013 0.002 PHE B1047 TYR 0.021 0.002 TYR B1739 ARG 0.032 0.001 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 189 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 MET cc_start: 0.4571 (OUTLIER) cc_final: 0.3649 (pmm) REVERT: A 1128 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7139 (mt) REVERT: A 1390 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8321 (pp) REVERT: A 1754 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8144 (m) REVERT: B 684 MET cc_start: 0.4756 (OUTLIER) cc_final: 0.3704 (pmm) REVERT: B 1128 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7003 (mt) REVERT: B 1390 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8398 (pp) REVERT: B 1754 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8153 (m) REVERT: B 1810 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7524 (ptpp) outliers start: 123 outliers final: 64 residues processed: 290 average time/residue: 0.3545 time to fit residues: 175.3518 Evaluate side-chains 250 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 177 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2027 MET Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1268 GLU Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1394 ASP Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1799 ASP Chi-restraints excluded: chain B residue 1810 LYS Chi-restraints excluded: chain B residue 1850 ILE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2020 ILE Chi-restraints excluded: chain B residue 2027 MET Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2267 THR Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 4.9990 chunk 311 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 346 optimal weight: 0.3980 chunk 287 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 181 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1758 HIS A2476 ASN ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28782 Z= 0.172 Angle : 0.580 10.010 38968 Z= 0.288 Chirality : 0.042 0.158 4544 Planarity : 0.004 0.046 4891 Dihedral : 6.088 87.100 3910 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.04 % Allowed : 18.53 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.99 (0.14), residues: 3554 helix: -0.94 (0.15), residues: 1136 sheet: -2.85 (0.21), residues: 544 loop : -2.40 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B2376 HIS 0.004 0.001 HIS B2173 PHE 0.012 0.001 PHE A1321 TYR 0.016 0.001 TYR B1739 ARG 0.004 0.000 ARG A1866 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 196 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 MET cc_start: 0.4759 (OUTLIER) cc_final: 0.3704 (pmm) REVERT: A 1390 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8181 (pp) REVERT: A 1731 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7307 (ptt90) REVERT: A 1754 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8096 (m) REVERT: A 1810 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7639 (ptpp) REVERT: B 684 MET cc_start: 0.4635 (OUTLIER) cc_final: 0.3503 (pmm) REVERT: B 1390 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8368 (pp) REVERT: B 1754 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8118 (m) outliers start: 95 outliers final: 64 residues processed: 272 average time/residue: 0.3489 time to fit residues: 159.7074 Evaluate side-chains 254 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 182 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1216 HIS Chi-restraints excluded: chain A residue 1240 LYS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1731 ARG Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2469 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1268 GLU Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1702 MET Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1799 ASP Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2020 ILE Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2331 THR Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Chi-restraints excluded: chain B residue 2469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 252 optimal weight: 0.6980 chunk 195 optimal weight: 0.2980 chunk 291 optimal weight: 0.0870 chunk 193 optimal weight: 5.9990 chunk 345 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 28782 Z= 0.160 Angle : 0.564 9.698 38968 Z= 0.279 Chirality : 0.042 0.188 4544 Planarity : 0.004 0.046 4891 Dihedral : 5.845 80.122 3910 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.17 % Allowed : 18.59 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.72 (0.14), residues: 3554 helix: -0.64 (0.16), residues: 1134 sheet: -2.75 (0.21), residues: 574 loop : -2.24 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B2376 HIS 0.004 0.001 HIS B 669 PHE 0.014 0.001 PHE B2326 TYR 0.018 0.001 TYR A 707 ARG 0.002 0.000 ARG A1866 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 199 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 MET cc_start: 0.4587 (OUTLIER) cc_final: 0.3554 (pmm) REVERT: A 787 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7512 (tp) REVERT: A 1390 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8109 (pp) REVERT: A 1754 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8016 (m) REVERT: A 1810 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7636 (ptpp) REVERT: B 684 MET cc_start: 0.4541 (OUTLIER) cc_final: 0.3317 (pmm) REVERT: B 1390 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8277 (pp) REVERT: B 1754 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8079 (m) REVERT: B 1869 MET cc_start: 0.4871 (tpt) cc_final: 0.4474 (mmm) outliers start: 99 outliers final: 71 residues processed: 279 average time/residue: 0.3570 time to fit residues: 167.9135 Evaluate side-chains 263 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 184 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2469 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1799 ASP Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2020 ILE Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2331 THR Chi-restraints excluded: chain B residue 2372 VAL Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Chi-restraints excluded: chain B residue 2469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 235 optimal weight: 0.0770 chunk 170 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 271 optimal weight: 4.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1926 HIS ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28782 Z= 0.152 Angle : 0.560 12.432 38968 Z= 0.276 Chirality : 0.042 0.153 4544 Planarity : 0.004 0.049 4891 Dihedral : 5.698 74.097 3910 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.78 % Allowed : 19.58 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.58 (0.14), residues: 3554 helix: -0.46 (0.16), residues: 1144 sheet: -2.84 (0.20), residues: 580 loop : -2.15 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B2376 HIS 0.003 0.001 HIS A2173 PHE 0.015 0.001 PHE A1585 TYR 0.019 0.001 TYR B1527 ARG 0.003 0.000 ARG A1866 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 197 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 MET cc_start: 0.4696 (OUTLIER) cc_final: 0.3558 (pmm) REVERT: A 787 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7467 (tp) REVERT: A 1390 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8162 (pp) REVERT: A 1719 MET cc_start: 0.7136 (mpp) cc_final: 0.6927 (mpp) REVERT: A 1754 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8009 (m) REVERT: A 1810 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7661 (ptpp) REVERT: A 2315 MET cc_start: 0.4504 (tmm) cc_final: 0.3919 (tmm) REVERT: B 684 MET cc_start: 0.4759 (OUTLIER) cc_final: 0.3621 (pmm) REVERT: B 1390 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8251 (pp) REVERT: B 1754 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8069 (m) outliers start: 87 outliers final: 63 residues processed: 267 average time/residue: 0.3520 time to fit residues: 158.9876 Evaluate side-chains 254 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 183 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1388 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1799 ASP Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2020 ILE Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2455 VAL Chi-restraints excluded: chain B residue 2469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 chunk 301 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 252 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 290 optimal weight: 0.4980 chunk 304 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28782 Z= 0.245 Angle : 0.607 11.814 38968 Z= 0.297 Chirality : 0.044 0.151 4544 Planarity : 0.004 0.048 4891 Dihedral : 5.792 69.568 3910 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.85 % Allowed : 19.87 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.56 (0.14), residues: 3554 helix: -0.47 (0.16), residues: 1142 sheet: -2.78 (0.20), residues: 568 loop : -2.15 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B2168 HIS 0.003 0.001 HIS B1039 PHE 0.014 0.001 PHE B1585 TYR 0.021 0.001 TYR A1739 ARG 0.005 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 189 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 MET cc_start: 0.4549 (OUTLIER) cc_final: 0.3382 (pmm) REVERT: A 787 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7511 (tp) REVERT: A 1390 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8228 (pp) REVERT: A 1754 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8037 (m) REVERT: A 1810 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7705 (ptpp) REVERT: A 2315 MET cc_start: 0.4683 (tmm) cc_final: 0.3350 (tmm) REVERT: B 684 MET cc_start: 0.4594 (OUTLIER) cc_final: 0.3725 (pmm) REVERT: B 1390 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8374 (pp) REVERT: B 1754 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8115 (m) outliers start: 89 outliers final: 71 residues processed: 260 average time/residue: 0.3532 time to fit residues: 154.7577 Evaluate side-chains 262 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 183 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2118 ASN Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1647 THR Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1799 ASP Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1916 LEU Chi-restraints excluded: chain B residue 1944 MET Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2020 ILE Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2118 ASN Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2372 VAL Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2455 VAL 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: 8.9990 chunk 207 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 356 optimal weight: 0.8980 chunk 328 optimal weight: 10.0000 chunk 284 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 219 optimal weight: 0.0040 chunk 174 optimal weight: 9.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 HIS ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28782 Z= 0.160 Angle : 0.567 11.648 38968 Z= 0.279 Chirality : 0.042 0.147 4544 Planarity : 0.004 0.049 4891 Dihedral : 5.645 63.473 3910 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.43 % Allowed : 20.42 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.44 (0.14), residues: 3554 helix: -0.36 (0.16), residues: 1148 sheet: -2.77 (0.20), residues: 562 loop : -2.07 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B2316 HIS 0.003 0.001 HIS A2173 PHE 0.015 0.001 PHE A1585 TYR 0.019 0.001 TYR A1739 ARG 0.013 0.000 ARG A2523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 191 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 MET cc_start: 0.4487 (OUTLIER) cc_final: 0.3205 (pmm) REVERT: A 787 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7475 (tp) REVERT: A 1390 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8122 (pp) REVERT: A 1754 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.8023 (m) REVERT: A 1810 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7673 (ptpp) REVERT: B 684 MET cc_start: 0.4471 (OUTLIER) cc_final: 0.3752 (pmm) REVERT: B 1390 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8371 (pp) REVERT: B 1754 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8071 (m) outliers start: 76 outliers final: 65 residues processed: 252 average time/residue: 0.3516 time to fit residues: 149.4018 Evaluate side-chains 255 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 182 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2458 MET Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1519 VAL Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1754 VAL Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1799 ASP Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2020 ILE Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2118 ASN Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2372 VAL Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2455 VAL Chi-restraints excluded: chain B residue 2458 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 0.0270 chunk 302 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 284 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 292 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.138637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.105909 restraints weight = 54708.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.104257 restraints weight = 41753.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.105195 restraints weight = 47303.661| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28782 Z= 0.175 Angle : 0.577 11.230 38968 Z= 0.282 Chirality : 0.042 0.145 4544 Planarity : 0.004 0.048 4891 Dihedral : 5.588 59.089 3910 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.59 % Allowed : 20.38 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.42 (0.14), residues: 3554 helix: -0.36 (0.16), residues: 1162 sheet: -2.74 (0.21), residues: 564 loop : -2.06 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A2168 HIS 0.006 0.001 HIS A 669 PHE 0.015 0.001 PHE A1585 TYR 0.018 0.001 TYR A1739 ARG 0.013 0.000 ARG B2523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5226.49 seconds wall clock time: 97 minutes 4.29 seconds (5824.29 seconds total)