Starting phenix.real_space_refine on Fri Dec 8 11:27:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzo_0791/12_2023/6kzo_0791_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzo_0791/12_2023/6kzo_0791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzo_0791/12_2023/6kzo_0791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzo_0791/12_2023/6kzo_0791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzo_0791/12_2023/6kzo_0791_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kzo_0791/12_2023/6kzo_0791_neut.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 7 5.49 5 S 64 5.16 5 C 5503 2.51 5 N 1260 2.21 5 O 1402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 747": "NH1" <-> "NH2" Residue "A GLU 763": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A ARG 1284": "NH1" <-> "NH2" Residue "A ARG 1364": "NH1" <-> "NH2" Residue "A ARG 1367": "NH1" <-> "NH2" Residue "A ARG 1371": "NH1" <-> "NH2" Residue "A ARG 1438": "NH1" <-> "NH2" Residue "A ARG 1441": "NH1" <-> "NH2" Residue "A ARG 1686": "NH1" <-> "NH2" Residue "A ARG 1692": "NH1" <-> "NH2" Residue "A ARG 1695": "NH1" <-> "NH2" Residue "A ARG 1763": "NH1" <-> "NH2" Residue "A ARG 1790": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8238 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 8238 Unusual residues: {' CA': 2, '3PE': 13, 'NAG': 5, 'Y01': 2} Classifications: {'peptide': 967, 'undetermined': 22} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 938, None: 22} Not linked: pdbres="GLU A1837 " pdbres=" CA A2301 " Not linked: pdbres=" CA A2301 " pdbres=" CA A2302 " Not linked: pdbres=" CA A2302 " pdbres="NAG A2303 " Not linked: pdbres="NAG A2303 " pdbres="NAG A2304 " Not linked: pdbres="NAG A2304 " pdbres="NAG A2305 " ... (remaining 17 not shown) Chain breaks: 12 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'3PE:plan-1': 6, '3PE:plan-2': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 5.09, per 1000 atoms: 0.62 Number of scatterers: 8238 At special positions: 0 Unit cell: (111.282, 121.101, 97.099, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 64 16.00 P 7 15.00 O 1402 8.00 N 1260 7.00 C 5503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 889 " distance=1.95 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 282 " distance=1.91 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1432 " distance=2.02 Simple disulfide: pdb=" SG CYS A1747 " - pdb=" SG CYS A1753 " distance=2.02 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 Links applied NAG-ASN " NAG A2303 " - " ASN A 246 " " NAG A2304 " - " ASN A 322 " " NAG A2305 " - " ASN A1425 " " NAG A2306 " - " ASN A1428 " " NAG A2307 " - " ASN A1675 " Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 2 sheets defined 76.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.695A pdb=" N ILE A 86 " --> pdb=" O TRP A 82 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 138 removed outlier: 3.554A pdb=" N ASP A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.506A pdb=" N LEU A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.781A pdb=" N VAL A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 178 through 182' Processing helix chain 'A' and resid 183 through 188 Proline residue: A 187 - end of helix Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.080A pdb=" N ARG A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.917A pdb=" N LEU A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 233 removed outlier: 3.503A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.744A pdb=" N GLN A 318 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 320 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 352 removed outlier: 3.611A pdb=" N TRP A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.904A pdb=" N ILE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.705A pdb=" N PHE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.575A pdb=" N GLN A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 761 removed outlier: 3.611A pdb=" N ILE A 751 " --> pdb=" O ARG A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 794 removed outlier: 4.039A pdb=" N GLU A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.662A pdb=" N ILE A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 804 " --> pdb=" O PHE A 800 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 820 removed outlier: 3.805A pdb=" N ILE A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 810 " --> pdb=" O PRO A 806 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 815 " --> pdb=" O ASP A 811 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 removed outlier: 3.652A pdb=" N ARG A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.905A pdb=" N VAL A 841 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 843 " --> pdb=" O ARG A 840 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 846 " --> pdb=" O LYS A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 861 removed outlier: 3.525A pdb=" N VAL A 856 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 861 " --> pdb=" O VAL A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 887 removed outlier: 3.879A pdb=" N THR A 867 " --> pdb=" O ASP A 863 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 868 " --> pdb=" O ASN A 864 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 874 " --> pdb=" O MET A 870 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 3.577A pdb=" N MET A 884 " --> pdb=" O SER A 880 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 921 removed outlier: 3.593A pdb=" N VAL A 914 " --> pdb=" O LEU A 910 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 915 " --> pdb=" O TRP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 936 removed outlier: 4.002A pdb=" N VAL A 928 " --> pdb=" O ASP A 924 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 931 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 939 No H-bonds generated for 'chain 'A' and resid 937 through 939' Processing helix chain 'A' and resid 940 through 967 removed outlier: 4.120A pdb=" N PHE A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 958 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1273 removed outlier: 3.707A pdb=" N ILE A1262 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A1268 " --> pdb=" O PHE A1264 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1310 removed outlier: 3.957A pdb=" N ILE A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A1308 " --> pdb=" O VAL A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1342 removed outlier: 3.675A pdb=" N LEU A1326 " --> pdb=" O SER A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1345 No H-bonds generated for 'chain 'A' and resid 1343 through 1345' Processing helix chain 'A' and resid 1351 through 1361 Processing helix chain 'A' and resid 1362 through 1365 Proline residue: A1365 - end of helix No H-bonds generated for 'chain 'A' and resid 1362 through 1365' Processing helix chain 'A' and resid 1366 through 1372 removed outlier: 4.216A pdb=" N SER A1370 " --> pdb=" O LEU A1366 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A1371 " --> pdb=" O ARG A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1387 removed outlier: 3.520A pdb=" N VAL A1378 " --> pdb=" O GLY A1374 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1411 removed outlier: 3.591A pdb=" N VAL A1394 " --> pdb=" O GLY A1390 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A1395 " --> pdb=" O ASN A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1433 Processing helix chain 'A' and resid 1448 through 1462 removed outlier: 3.890A pdb=" N MET A1454 " --> pdb=" O GLY A1450 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A1457 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A1459 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1460 " --> pdb=" O LEU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1474 removed outlier: 3.533A pdb=" N ILE A1468 " --> pdb=" O GLY A1464 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP A1471 " --> pdb=" O ASP A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1489 No H-bonds generated for 'chain 'A' and resid 1487 through 1489' Processing helix chain 'A' and resid 1490 through 1518 removed outlier: 3.570A pdb=" N PHE A1494 " --> pdb=" O MET A1490 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A1496 " --> pdb=" O LEU A1492 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A1497 " --> pdb=" O TYR A1493 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A1500 " --> pdb=" O SER A1496 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A1503 " --> pdb=" O LEU A1499 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A1516 " --> pdb=" O VAL A1512 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A1517 " --> pdb=" O VAL A1513 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS A1518 " --> pdb=" O VAL A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1606 removed outlier: 3.677A pdb=" N GLY A1596 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1638 removed outlier: 3.698A pdb=" N ILE A1626 " --> pdb=" O ILE A1622 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A1629 " --> pdb=" O TYR A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1654 through 1676 removed outlier: 3.618A pdb=" N THR A1668 " --> pdb=" O ILE A1664 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A1673 " --> pdb=" O LEU A1669 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A1675 " --> pdb=" O GLU A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 removed outlier: 3.703A pdb=" N ILE A1685 " --> pdb=" O ASN A1681 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1701 Processing helix chain 'A' and resid 1703 through 1716 removed outlier: 3.579A pdb=" N ARG A1707 " --> pdb=" O ALA A1703 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A1712 " --> pdb=" O ALA A1708 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A1713 " --> pdb=" O LEU A1709 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A1714 " --> pdb=" O LEU A1710 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A1716 " --> pdb=" O THR A1712 " (cutoff:3.500A) Processing helix chain 'A' and resid 1716 through 1742 removed outlier: 3.654A pdb=" N GLU A1740 " --> pdb=" O ALA A1736 " (cutoff:3.500A) Processing helix chain 'A' and resid 1766 through 1778 removed outlier: 3.872A pdb=" N LEU A1772 " --> pdb=" O ALA A1768 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A1773 " --> pdb=" O PHE A1769 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A1774 " --> pdb=" O LEU A1770 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A1776 " --> pdb=" O LEU A1772 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1787 removed outlier: 3.609A pdb=" N ILE A1784 " --> pdb=" O ASN A1780 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A1787 " --> pdb=" O GLY A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1837 removed outlier: 3.577A pdb=" N ILE A1806 " --> pdb=" O VAL A1802 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A1812 " --> pdb=" O PHE A1808 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1817 " --> pdb=" O LEU A1813 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A1823 " --> pdb=" O LEU A1819 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A1825 " --> pdb=" O ASN A1821 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A1829 " --> pdb=" O ALA A1825 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A1833 " --> pdb=" O LYS A1829 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A1834 " --> pdb=" O HIS A1830 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A1835 " --> pdb=" O LEU A1831 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A1836 " --> pdb=" O GLU A1832 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A1837 " --> pdb=" O GLU A1833 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 242 Processing sheet with id=AA2, first strand: chain 'A' and resid 1416 through 1419 444 hydrogen bonds defined for protein. 1284 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: 2.35 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1227 1.31 - 1.43: 2186 1.43 - 1.56: 4835 1.56 - 1.68: 34 1.68 - 1.81: 112 Bond restraints: 8394 Sorted by residual: bond pdb=" CAI Y01 A2321 " pdb=" CAZ Y01 A2321 " ideal model delta sigma weight residual 1.332 1.690 -0.358 2.00e-02 2.50e+03 3.21e+02 bond pdb=" CAI Y01 A2322 " pdb=" CAZ Y01 A2322 " ideal model delta sigma weight residual 1.332 1.688 -0.356 2.00e-02 2.50e+03 3.17e+02 bond pdb=" CAP Y01 A2321 " pdb=" CAQ Y01 A2321 " ideal model delta sigma weight residual 1.541 1.726 -0.185 2.00e-02 2.50e+03 8.52e+01 bond pdb=" CAP Y01 A2322 " pdb=" CAQ Y01 A2322 " ideal model delta sigma weight residual 1.541 1.723 -0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" C21 3PE A2312 " pdb=" O21 3PE A2312 " ideal model delta sigma weight residual 1.316 1.465 -0.149 2.00e-02 2.50e+03 5.57e+01 ... (remaining 8389 not shown) Histogram of bond angle deviations from ideal: 95.19 - 103.01: 74 103.01 - 110.83: 2877 110.83 - 118.65: 3813 118.65 - 126.47: 4437 126.47 - 134.29: 92 Bond angle restraints: 11293 Sorted by residual: angle pdb=" N ALA A 334 " pdb=" CA ALA A 334 " pdb=" C ALA A 334 " ideal model delta sigma weight residual 111.36 122.16 -10.80 1.09e+00 8.42e-01 9.82e+01 angle pdb=" N VAL A1674 " pdb=" CA VAL A1674 " pdb=" C VAL A1674 " ideal model delta sigma weight residual 110.53 117.74 -7.21 9.40e-01 1.13e+00 5.89e+01 angle pdb=" N ASP A1447 " pdb=" CA ASP A1447 " pdb=" C ASP A1447 " ideal model delta sigma weight residual 111.14 119.16 -8.02 1.08e+00 8.57e-01 5.51e+01 angle pdb=" N GLU A 256 " pdb=" CA GLU A 256 " pdb=" C GLU A 256 " ideal model delta sigma weight residual 111.28 119.25 -7.97 1.09e+00 8.42e-01 5.35e+01 angle pdb=" N GLU A 327 " pdb=" CA GLU A 327 " pdb=" C GLU A 327 " ideal model delta sigma weight residual 111.28 119.13 -7.85 1.09e+00 8.42e-01 5.18e+01 ... (remaining 11288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.82: 4908 27.82 - 55.63: 277 55.63 - 83.45: 30 83.45 - 111.27: 9 111.27 - 139.08: 3 Dihedral angle restraints: 5227 sinusoidal: 2415 harmonic: 2812 Sorted by residual: dihedral pdb=" CB CYS A 271 " pdb=" SG CYS A 271 " pdb=" SG CYS A 282 " pdb=" CB CYS A 282 " ideal model delta sinusoidal sigma weight residual -86.00 -173.82 87.82 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A1747 " pdb=" SG CYS A1747 " pdb=" SG CYS A1753 " pdb=" CB CYS A1753 " ideal model delta sinusoidal sigma weight residual 93.00 139.61 -46.61 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA ASP A1787 " pdb=" C ASP A1787 " pdb=" N THR A1788 " pdb=" CA THR A1788 " ideal model delta harmonic sigma weight residual 180.00 154.26 25.74 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 5224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 1290 0.261 - 0.522: 22 0.522 - 0.783: 2 0.783 - 1.044: 1 1.044 - 1.304: 2 Chirality restraints: 1317 Sorted by residual: chirality pdb=" C1 NAG A2305 " pdb=" ND2 ASN A1425 " pdb=" C2 NAG A2305 " pdb=" O5 NAG A2305 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.25e+01 chirality pdb=" C1 NAG A2307 " pdb=" ND2 ASN A1675 " pdb=" C2 NAG A2307 " pdb=" O5 NAG A2307 " both_signs ideal model delta sigma weight residual False -2.40 -1.32 -1.08 2.00e-01 2.50e+01 2.93e+01 chirality pdb=" C1 NAG A2306 " pdb=" ND2 ASN A1428 " pdb=" C2 NAG A2306 " pdb=" O5 NAG A2306 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 1314 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1428 " -0.014 2.00e-02 2.50e+03 3.12e-01 1.21e+03 pdb=" CG ASN A1428 " -0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN A1428 " 0.263 2.00e-02 2.50e+03 pdb=" ND2 ASN A1428 " -0.526 2.00e-02 2.50e+03 pdb=" C1 NAG A2306 " 0.363 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1425 " -0.203 2.00e-02 2.50e+03 2.14e-01 5.73e+02 pdb=" CG ASN A1425 " 0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN A1425 " 0.071 2.00e-02 2.50e+03 pdb=" ND2 ASN A1425 " 0.316 2.00e-02 2.50e+03 pdb=" C1 NAG A2305 " -0.274 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2306 " -0.204 2.00e-02 2.50e+03 1.74e-01 3.79e+02 pdb=" C7 NAG A2306 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG A2306 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG A2306 " 0.287 2.00e-02 2.50e+03 pdb=" O7 NAG A2306 " -0.158 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1065 2.74 - 3.28: 8442 3.28 - 3.82: 12205 3.82 - 4.36: 15371 4.36 - 4.90: 25841 Nonbonded interactions: 62924 Sorted by model distance: nonbonded pdb=" OD1 ASN A 213 " pdb=" C GLY A1705 " model vdw 2.196 3.270 nonbonded pdb=" N ASP A 907 " pdb=" OD1 ASP A 907 " model vdw 2.205 2.520 nonbonded pdb=" OD1 ASN A1425 " pdb=" O5 NAG A2305 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN A 213 " pdb=" N MET A1706 " model vdw 2.246 2.520 nonbonded pdb=" O LEU A1710 " pdb=" CG1 VAL A1713 " model vdw 2.278 3.460 ... (remaining 62919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.010 Extract box with map and model: 7.010 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 25.680 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.014 0.358 8394 Z= 0.870 Angle : 1.415 11.337 11293 Z= 0.841 Chirality : 0.104 1.304 1317 Planarity : 0.011 0.174 1340 Dihedral : 16.980 139.084 3383 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 36.78 Ramachandran Plot: Outliers : 0.74 % Allowed : 3.29 % Favored : 95.96 % Rotamer: Outliers : 9.01 % Allowed : 12.98 % Favored : 78.01 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % 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: -1.32 (0.27), residues: 941 helix: -0.54 (0.20), residues: 685 sheet: 0.10 (1.60), residues: 10 loop : -1.47 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 233 HIS 0.007 0.002 HIS A1609 PHE 0.029 0.003 PHE A1731 TYR 0.028 0.003 TYR A 258 ARG 0.015 0.001 ARG A1774 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 199 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 39 residues processed: 264 average time/residue: 0.2012 time to fit residues: 72.1310 Evaluate side-chains 181 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 142 time to evaluate : 0.912 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 2 residues processed: 39 average time/residue: 0.0990 time to fit residues: 7.6445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN A 773 ASN A 852 GLN A 854 GLN A 952 ASN A1266 ASN A1291 ASN A1409 GLN A1445 ASN A1481 GLN A1486 HIS A1722 ASN A1780 ASN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8394 Z= 0.224 Angle : 0.729 9.989 11293 Z= 0.358 Chirality : 0.048 0.570 1317 Planarity : 0.006 0.072 1340 Dihedral : 12.134 89.438 1597 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.13 % Rotamer: Outliers : 3.04 % Allowed : 18.25 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.27), residues: 941 helix: 0.20 (0.20), residues: 679 sheet: -2.05 (0.92), residues: 22 loop : -1.08 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1439 HIS 0.005 0.001 HIS A1442 PHE 0.023 0.002 PHE A 875 TYR 0.027 0.002 TYR A 764 ARG 0.004 0.001 ARG A1424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 0.830 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 203 average time/residue: 0.1857 time to fit residues: 54.1901 Evaluate side-chains 171 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 0.921 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.0799 time to fit residues: 3.3106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 349 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8394 Z= 0.223 Angle : 0.666 9.797 11293 Z= 0.322 Chirality : 0.045 0.488 1317 Planarity : 0.005 0.063 1340 Dihedral : 11.887 87.463 1597 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 2.92 % Allowed : 21.05 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.27), residues: 941 helix: 0.59 (0.20), residues: 687 sheet: -2.41 (0.91), residues: 22 loop : -1.18 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1439 HIS 0.003 0.001 HIS A1830 PHE 0.019 0.002 PHE A 385 TYR 0.022 0.001 TYR A 764 ARG 0.004 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 0.950 Fit side-chains outliers start: 25 outliers final: 14 residues processed: 181 average time/residue: 0.1805 time to fit residues: 46.4004 Evaluate side-chains 163 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 0.939 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.0781 time to fit residues: 3.2185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1516 ASN A1816 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8394 Z= 0.215 Angle : 0.625 8.987 11293 Z= 0.306 Chirality : 0.043 0.323 1317 Planarity : 0.005 0.059 1340 Dihedral : 11.400 89.834 1597 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 3.04 % Allowed : 22.57 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.28), residues: 941 helix: 0.90 (0.20), residues: 684 sheet: -2.34 (0.91), residues: 22 loop : -1.14 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1439 HIS 0.003 0.001 HIS A1442 PHE 0.017 0.001 PHE A 123 TYR 0.023 0.001 TYR A 764 ARG 0.004 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 0.868 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 171 average time/residue: 0.1691 time to fit residues: 41.7666 Evaluate side-chains 155 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.870 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.0800 time to fit residues: 2.7032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 0.0020 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8394 Z= 0.206 Angle : 0.611 9.013 11293 Z= 0.297 Chirality : 0.042 0.323 1317 Planarity : 0.004 0.052 1340 Dihedral : 11.093 88.493 1597 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 3.16 % Allowed : 22.57 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.28), residues: 941 helix: 1.06 (0.20), residues: 684 sheet: -2.32 (0.94), residues: 22 loop : -1.06 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1439 HIS 0.005 0.001 HIS A 765 PHE 0.018 0.001 PHE A 123 TYR 0.021 0.001 TYR A 764 ARG 0.003 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 0.912 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 165 average time/residue: 0.1769 time to fit residues: 42.3125 Evaluate side-chains 158 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 0.862 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.0808 time to fit residues: 3.2426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.0270 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8394 Z= 0.203 Angle : 0.618 11.184 11293 Z= 0.297 Chirality : 0.042 0.311 1317 Planarity : 0.004 0.049 1340 Dihedral : 10.912 87.703 1597 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.28 % Rotamer: Outliers : 1.99 % Allowed : 23.39 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.28), residues: 941 helix: 1.12 (0.20), residues: 689 sheet: -2.37 (1.38), residues: 12 loop : -0.84 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.003 0.001 HIS A 765 PHE 0.019 0.001 PHE A 123 TYR 0.028 0.001 TYR A 764 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 0.973 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 161 average time/residue: 0.1787 time to fit residues: 41.2550 Evaluate side-chains 154 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.919 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.0795 time to fit residues: 2.2823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1653 ASN A1816 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8394 Z= 0.197 Angle : 0.612 12.377 11293 Z= 0.293 Chirality : 0.041 0.303 1317 Planarity : 0.004 0.049 1340 Dihedral : 10.846 86.385 1597 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.28 % Rotamer: Outliers : 2.11 % Allowed : 23.74 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.28), residues: 941 helix: 1.27 (0.20), residues: 690 sheet: -2.53 (1.30), residues: 12 loop : -0.71 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.004 0.001 HIS A 765 PHE 0.020 0.001 PHE A 123 TYR 0.017 0.001 TYR A 764 ARG 0.005 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 0.875 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 159 average time/residue: 0.1798 time to fit residues: 41.0657 Evaluate side-chains 151 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 0.833 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.1335 time to fit residues: 3.2500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.0060 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.0030 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8394 Z= 0.171 Angle : 0.614 12.638 11293 Z= 0.293 Chirality : 0.040 0.287 1317 Planarity : 0.004 0.048 1340 Dihedral : 10.609 84.389 1597 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 1.52 % Allowed : 23.98 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.28), residues: 941 helix: 1.39 (0.20), residues: 690 sheet: -2.22 (1.38), residues: 12 loop : -0.66 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1439 HIS 0.003 0.001 HIS A 765 PHE 0.018 0.001 PHE A 875 TYR 0.024 0.001 TYR A 764 ARG 0.003 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 0.898 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 160 average time/residue: 0.1673 time to fit residues: 39.1228 Evaluate side-chains 153 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0766 time to fit residues: 2.1084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1816 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8394 Z= 0.182 Angle : 0.638 13.301 11293 Z= 0.300 Chirality : 0.040 0.290 1317 Planarity : 0.004 0.048 1340 Dihedral : 10.534 84.444 1597 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.28 % Rotamer: Outliers : 1.05 % Allowed : 25.03 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.28), residues: 941 helix: 1.47 (0.20), residues: 690 sheet: -2.60 (1.31), residues: 12 loop : -0.64 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1439 HIS 0.003 0.001 HIS A 765 PHE 0.018 0.001 PHE A 875 TYR 0.013 0.001 TYR A 764 ARG 0.002 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 0.918 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 152 average time/residue: 0.1769 time to fit residues: 38.9415 Evaluate side-chains 147 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0795 time to fit residues: 1.9690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.3980 chunk 56 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8394 Z= 0.192 Angle : 0.642 13.598 11293 Z= 0.304 Chirality : 0.041 0.294 1317 Planarity : 0.004 0.049 1340 Dihedral : 10.469 84.761 1597 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 0.58 % Allowed : 25.26 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.28), residues: 941 helix: 1.46 (0.20), residues: 690 sheet: -3.03 (1.23), residues: 12 loop : -0.62 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1439 HIS 0.004 0.001 HIS A 765 PHE 0.018 0.001 PHE A 875 TYR 0.024 0.001 TYR A 764 ARG 0.001 0.000 ARG A 189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 0.932 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 148 average time/residue: 0.1767 time to fit residues: 37.7487 Evaluate side-chains 149 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.0785 time to fit residues: 1.7764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.0370 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1816 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116319 restraints weight = 11909.838| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.91 r_work: 0.3257 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8394 Z= 0.181 Angle : 0.645 13.588 11293 Z= 0.304 Chirality : 0.040 0.288 1317 Planarity : 0.004 0.048 1340 Dihedral : 10.307 84.017 1597 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 0.82 % Allowed : 25.61 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.28), residues: 941 helix: 1.53 (0.20), residues: 690 sheet: -3.40 (1.11), residues: 12 loop : -0.58 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1439 HIS 0.003 0.001 HIS A 765 PHE 0.018 0.001 PHE A 875 TYR 0.016 0.001 TYR A 361 ARG 0.002 0.000 ARG A 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.27 seconds wall clock time: 37 minutes 0.99 seconds (2220.99 seconds total)