Starting phenix.real_space_refine on Sun Feb 18 09:41:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw5_13675/02_2024/7pw5_13675_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw5_13675/02_2024/7pw5_13675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw5_13675/02_2024/7pw5_13675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw5_13675/02_2024/7pw5_13675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw5_13675/02_2024/7pw5_13675_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw5_13675/02_2024/7pw5_13675_neut_updated.pdb" } resolution = 3.4 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= 0.007 sd= 0.058 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: 7 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 113 5.16 5 Cl 1 4.86 5 C 13837 2.51 5 N 3811 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 840": "OE1" <-> "OE2" Residue "A ASP 2209": "OD1" <-> "OD2" Residue "A GLU 3655": "OE1" <-> "OE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B GLU 568": "OE1" <-> "OE2" Residue "B PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 588": "OE1" <-> "OE2" Residue "B GLU 591": "OE1" <-> "OE2" Residue "B PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 625": "OD1" <-> "OD2" Residue "B TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 638": "OE1" <-> "OE2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 745": "OE1" <-> "OE2" Residue "B TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 850": "OE1" <-> "OE2" Residue "B TYR 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 852": "OE1" <-> "OE2" Residue "B GLU 877": "OE1" <-> "OE2" Residue "B PHE 911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 940": "OE1" <-> "OE2" Residue "B GLU 943": "OE1" <-> "OE2" Residue "B PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 963": "OE1" <-> "OE2" Residue "B GLU 972": "OE1" <-> "OE2" Residue "B TYR 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C GLU 514": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21548 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1944, 13724 Classifications: {'peptide': 1944} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 542} Link IDs: {'PTRANS': 61, 'TRANS': 1882} Chain breaks: 39 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1531 Unresolved non-hydrogen angles: 2011 Unresolved non-hydrogen dihedrals: 1110 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 3, 'ASN:plan1': 17, 'TYR:plan': 4, 'UNK:plan-1': 195, 'TRP:plan': 4, 'ASP:plan': 47, 'PHE:plan': 6, 'GLU:plan': 70, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 912 Chain: "B" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5296 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 646} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 249 Chain: "C" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2421 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 292} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'88C': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG C 602 " occ=0.00 Time building chain proxies: 12.02, per 1000 atoms: 0.56 Number of scatterers: 21548 At special positions: 0 Unit cell: (125.978, 160.877, 182.157, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 113 16.00 P 9 15.00 Mg 1 11.99 O 3776 8.00 N 3811 7.00 C 13837 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.34 Conformation dependent library (CDL) restraints added in 4.3 seconds 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5684 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 12 sheets defined 59.1% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.64 Creating SS restraints... Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.776A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.516A pdb=" N UNK A 171 " --> pdb=" O UNK A 167 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N UNK A 172 " --> pdb=" O UNK A 168 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N UNK A 173 " --> pdb=" O UNK A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 208 through 220 removed outlier: 4.256A pdb=" N UNK A 220 " --> pdb=" O UNK A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.627A pdb=" N UNK A 234 " --> pdb=" O UNK A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 271 through 284 removed outlier: 3.912A pdb=" N UNK A 284 " --> pdb=" O UNK A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.987A pdb=" N UNK A 303 " --> pdb=" O UNK A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.673A pdb=" N THR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 356 through 375 removed outlier: 4.115A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 429 through 443 Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 476 through 488 removed outlier: 3.665A pdb=" N ASN A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.910A pdb=" N ILE A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 558 through 582 removed outlier: 4.056A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 592 No H-bonds generated for 'chain 'A' and resid 590 through 592' Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 604 through 622 removed outlier: 3.831A pdb=" N THR A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 653 through 656 No H-bonds generated for 'chain 'A' and resid 653 through 656' Processing helix chain 'A' and resid 658 through 678 removed outlier: 3.756A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS A 675 " --> pdb=" O HIS A 671 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 676 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N HIS A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE A 678 " --> pdb=" O ARG A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 702 No H-bonds generated for 'chain 'A' and resid 699 through 702' Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 725 through 744 removed outlier: 3.738A pdb=" N ARG A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 744 " --> pdb=" O VAL A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 752 Processing helix chain 'A' and resid 755 through 767 Processing helix chain 'A' and resid 773 through 785 Processing helix chain 'A' and resid 792 through 805 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 826 through 829 No H-bonds generated for 'chain 'A' and resid 826 through 829' Processing helix chain 'A' and resid 836 through 850 Processing helix chain 'A' and resid 859 through 870 Processing helix chain 'A' and resid 882 through 889 Processing helix chain 'A' and resid 903 through 907 removed outlier: 4.113A pdb=" N LYS A 907 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 926 Processing helix chain 'A' and resid 936 through 955 removed outlier: 4.002A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 998 removed outlier: 4.069A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 3.899A pdb=" N THR A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1040 removed outlier: 4.515A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1057 Processing helix chain 'A' and resid 1069 through 1082 Processing helix chain 'A' and resid 1086 through 1098 removed outlier: 3.954A pdb=" N SER A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1115 removed outlier: 3.863A pdb=" N ASN A1108 " --> pdb=" O LEU A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1133 Processing helix chain 'A' and resid 1144 through 1150 Processing helix chain 'A' and resid 1180 through 1196 Processing helix chain 'A' and resid 1200 through 1217 Processing helix chain 'A' and resid 1228 through 1239 Processing helix chain 'A' and resid 1242 through 1251 removed outlier: 3.540A pdb=" N GLU A1247 " --> pdb=" O VAL A1243 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A1251 " --> pdb=" O GLU A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1304 Processing helix chain 'A' and resid 1318 through 1340 removed outlier: 3.883A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A1332 " --> pdb=" O SER A1328 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Proline residue: A1334 - end of helix removed outlier: 3.540A pdb=" N THR A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1340 " --> pdb=" O ARG A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1366 removed outlier: 3.608A pdb=" N SER A1365 " --> pdb=" O GLU A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1373 No H-bonds generated for 'chain 'A' and resid 1371 through 1373' Processing helix chain 'A' and resid 1379 through 1382 Processing helix chain 'A' and resid 1391 through 1409 removed outlier: 3.875A pdb=" N GLN A1395 " --> pdb=" O ARG A1391 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A1396 " --> pdb=" O PRO A1392 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A1403 " --> pdb=" O TYR A1399 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS A1409 " --> pdb=" O GLN A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1435 removed outlier: 3.517A pdb=" N ARG A1435 " --> pdb=" O PHE A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1449 Processing helix chain 'A' and resid 1459 through 1466 removed outlier: 3.555A pdb=" N VAL A1463 " --> pdb=" O ALA A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1494 Processing helix chain 'A' and resid 1497 through 1513 removed outlier: 4.069A pdb=" N LYS A1513 " --> pdb=" O ILE A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1534 Processing helix chain 'A' and resid 1540 through 1550 Processing helix chain 'A' and resid 1560 through 1569 Processing helix chain 'A' and resid 1589 through 1591 No H-bonds generated for 'chain 'A' and resid 1589 through 1591' Processing helix chain 'A' and resid 1596 through 1611 removed outlier: 4.159A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1636 Processing helix chain 'A' and resid 1647 through 1655 Processing helix chain 'A' and resid 1664 through 1674 removed outlier: 3.579A pdb=" N UNK A1674 " --> pdb=" O UNK A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1716 Processing helix chain 'A' and resid 1729 through 1741 removed outlier: 3.569A pdb=" N ASP A1738 " --> pdb=" O ARG A1734 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A1739 " --> pdb=" O LYS A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1758 removed outlier: 3.727A pdb=" N ASN A1758 " --> pdb=" O PHE A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1798 removed outlier: 3.526A pdb=" N MET A1787 " --> pdb=" O ASP A1783 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A1788 " --> pdb=" O MET A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1810 removed outlier: 3.864A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1828 Processing helix chain 'A' and resid 1836 through 1849 Processing helix chain 'A' and resid 1857 through 1864 Processing helix chain 'A' and resid 1925 through 1939 removed outlier: 4.029A pdb=" N CYS A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A1930 " --> pdb=" O MET A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1957 Processing helix chain 'A' and resid 1963 through 1977 Processing helix chain 'A' and resid 2007 through 2020 Processing helix chain 'A' and resid 2037 through 2043 Processing helix chain 'A' and resid 2047 through 2055 Processing helix chain 'A' and resid 2069 through 2082 Processing helix chain 'A' and resid 2161 through 2177 removed outlier: 3.549A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET A2176 " --> pdb=" O ILE A2172 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A2177 " --> pdb=" O VAL A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2180 through 2183 removed outlier: 3.819A pdb=" N GLN A2183 " --> pdb=" O ILE A2180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2180 through 2183' Processing helix chain 'A' and resid 2214 through 2231 Processing helix chain 'A' and resid 2249 through 2264 removed outlier: 3.545A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Proline residue: A2259 - end of helix Processing helix chain 'A' and resid 2277 through 2288 Processing helix chain 'A' and resid 2297 through 2303 Processing helix chain 'A' and resid 2307 through 2331 Processing helix chain 'A' and resid 2338 through 2340 No H-bonds generated for 'chain 'A' and resid 2338 through 2340' Processing helix chain 'A' and resid 2362 through 2364 No H-bonds generated for 'chain 'A' and resid 2362 through 2364' Processing helix chain 'A' and resid 2377 through 2383 removed outlier: 3.641A pdb=" N LEU A2383 " --> pdb=" O ILE A2379 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2405 Processing helix chain 'A' and resid 2407 through 2418 Processing helix chain 'A' and resid 3608 through 3621 Processing helix chain 'A' and resid 3633 through 3643 Processing helix chain 'A' and resid 3647 through 3650 No H-bonds generated for 'chain 'A' and resid 3647 through 3650' Processing helix chain 'A' and resid 3655 through 3657 No H-bonds generated for 'chain 'A' and resid 3655 through 3657' Processing helix chain 'B' and resid 8 through 11 No H-bonds generated for 'chain 'B' and resid 8 through 11' Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.588A pdb=" N ARG B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 205 removed outlier: 3.577A pdb=" N SER B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 244 removed outlier: 3.802A pdb=" N PHE B 227 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP B 231 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLY B 232 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU B 238 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.905A pdb=" N LYS B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 296 through 314 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 410 through 422 removed outlier: 4.254A pdb=" N HIS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 457 removed outlier: 3.816A pdb=" N ALA B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 484 removed outlier: 3.803A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 Proline residue: B 505 - end of helix Processing helix chain 'B' and resid 524 through 538 Processing helix chain 'B' and resid 544 through 556 removed outlier: 3.655A pdb=" N CYS B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR B 556 " --> pdb=" O HIS B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 630 Processing helix chain 'B' and resid 632 through 638 Processing helix chain 'B' and resid 774 through 776 No H-bonds generated for 'chain 'B' and resid 774 through 776' Processing helix chain 'B' and resid 839 through 841 No H-bonds generated for 'chain 'B' and resid 839 through 841' Processing helix chain 'B' and resid 879 through 883 Processing helix chain 'B' and resid 976 through 978 No H-bonds generated for 'chain 'B' and resid 976 through 978' Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 243 through 246 No H-bonds generated for 'chain 'C' and resid 243 through 246' Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 330 through 339 Processing helix chain 'C' and resid 376 through 378 No H-bonds generated for 'chain 'C' and resid 376 through 378' Processing helix chain 'C' and resid 381 through 395 removed outlier: 3.513A pdb=" N GLN C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 454 through 456 No H-bonds generated for 'chain 'C' and resid 454 through 456' Processing helix chain 'C' and resid 466 through 478 Processing helix chain 'C' and resid 492 through 507 Processing helix chain 'C' and resid 511 through 517 Processing sheet with id= A, first strand: chain 'A' and resid 2129 through 2131 removed outlier: 3.849A pdb=" N LYS A2138 " --> pdb=" O PHE A2154 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A2152 " --> pdb=" O LEU A2140 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 2211 through 2213 Processing sheet with id= C, first strand: chain 'B' and resid 336 through 339 removed outlier: 9.083A pdb=" N TYR B 337 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 267 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL B 339 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE B 269 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLY B 54 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 606 through 610 Processing sheet with id= E, first strand: chain 'B' and resid 646 through 648 removed outlier: 3.996A pdb=" N ASP B 646 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B 768 " --> pdb=" O ILE B 648 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 951 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU B 850 " --> pdb=" O MET B 908 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 910 " --> pdb=" O GLY B 848 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY B 848 " --> pdb=" O LEU B 910 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 912 " --> pdb=" O PHE B 846 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE B 846 " --> pdb=" O VAL B 912 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 914 " --> pdb=" O ARG B 844 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ARG B 844 " --> pdb=" O VAL B 914 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 849 through 852 removed outlier: 4.208A pdb=" N PHE B 849 " --> pdb=" O CYS B 861 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 890 through 892 Processing sheet with id= H, first strand: chain 'B' and resid 986 through 990 removed outlier: 4.588A pdb=" N ILE B 921 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 936 through 938 Processing sheet with id= J, first strand: chain 'B' and resid 960 through 962 removed outlier: 4.698A pdb=" N TYR B 960 " --> pdb=" O CYS B 967 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.260A pdb=" N LEU C 205 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU C 268 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 317 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU C 210 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE C 319 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS C 366 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL C 320 " --> pdb=" O HIS C 366 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 368 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLN C 322 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU C 370 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 181 through 184 removed outlier: 6.634A pdb=" N ILE C 256 " --> pdb=" O LEU C 183 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 3102 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: 9.19 Time building geometry restraints manager: 9.98 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: 3430 1.31 - 1.44: 5710 1.44 - 1.57: 12649 1.57 - 1.69: 11 1.69 - 1.82: 171 Bond restraints: 21971 Sorted by residual: bond pdb=" C28 88C A3702 " pdb=" N30 88C A3702 " ideal model delta sigma weight residual 1.352 1.453 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" CA PRO B 947 " pdb=" C PRO B 947 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.23e+01 bond pdb=" C13 88C A3702 " pdb=" N12 88C A3702 " ideal model delta sigma weight residual 1.364 1.456 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C22 88C A3702 " pdb=" C23 88C A3702 " ideal model delta sigma weight residual 1.476 1.386 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C17 88C A3702 " pdb=" C18 88C A3702 " ideal model delta sigma weight residual 1.480 1.391 0.089 2.00e-02 2.50e+03 1.98e+01 ... (remaining 21966 not shown) Histogram of bond angle deviations from ideal: 98.97 - 107.15: 750 107.15 - 115.33: 13510 115.33 - 123.51: 14906 123.51 - 131.69: 765 131.69 - 139.87: 50 Bond angle restraints: 29981 Sorted by residual: angle pdb=" N GLU A 746 " pdb=" CA GLU A 746 " pdb=" C GLU A 746 " ideal model delta sigma weight residual 113.30 104.51 8.79 1.34e+00 5.57e-01 4.30e+01 angle pdb=" OE1 GLN B 991 " pdb=" CD GLN B 991 " pdb=" NE2 GLN B 991 " ideal model delta sigma weight residual 122.60 116.74 5.86 1.00e+00 1.00e+00 3.44e+01 angle pdb=" CA PRO A1392 " pdb=" N PRO A1392 " pdb=" CD PRO A1392 " ideal model delta sigma weight residual 112.00 103.82 8.18 1.40e+00 5.10e-01 3.41e+01 angle pdb=" O07 88C A3702 " pdb=" S06 88C A3702 " pdb=" O08 88C A3702 " ideal model delta sigma weight residual 117.67 101.03 16.64 3.00e+00 1.11e-01 3.08e+01 angle pdb=" N VAL A 393 " pdb=" CA VAL A 393 " pdb=" C VAL A 393 " ideal model delta sigma weight residual 113.20 108.01 5.19 9.60e-01 1.09e+00 2.92e+01 ... (remaining 29976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 12899 34.64 - 69.28: 224 69.28 - 103.91: 18 103.91 - 138.55: 2 138.55 - 173.19: 3 Dihedral angle restraints: 13146 sinusoidal: 4477 harmonic: 8669 Sorted by residual: dihedral pdb=" CA ARG B 803 " pdb=" C ARG B 803 " pdb=" N THR B 804 " pdb=" CA THR B 804 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" O12 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O13 IHP A3701 " ideal model delta sinusoidal sigma weight residual 64.08 -109.11 173.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 60.90 -129.71 -169.39 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 3611 0.990 - 1.980: 0 1.980 - 2.969: 0 2.969 - 3.959: 0 3.959 - 4.949: 3 Chirality restraints: 3614 Sorted by residual: chirality pdb=" C2 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " both_signs ideal model delta sigma weight residual False -2.52 2.43 -4.95 2.00e-01 2.50e+01 6.12e+02 chirality pdb=" C4 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" C5 IHP A3701 " pdb=" O14 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.48 -2.38 4.86 2.00e-01 2.50e+01 5.90e+02 chirality pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C6 IHP A3701 " pdb=" O11 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.32 -2.50 4.81 2.00e-01 2.50e+01 5.79e+02 ... (remaining 3611 not shown) Planarity restraints: 3761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 777 " 0.103 2.00e-02 2.50e+03 6.00e-02 7.20e+01 pdb=" CG TYR B 777 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 777 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR B 777 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR B 777 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR B 777 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR B 777 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 777 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 634 " -0.078 2.00e-02 2.50e+03 4.40e-02 3.88e+01 pdb=" CG TYR B 634 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 634 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 634 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 TYR B 634 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR B 634 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 634 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 634 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 552 " 0.027 2.00e-02 2.50e+03 5.42e-02 2.94e+01 pdb=" C HIS B 552 " -0.094 2.00e-02 2.50e+03 pdb=" O HIS B 552 " 0.035 2.00e-02 2.50e+03 pdb=" N GLU B 553 " 0.031 2.00e-02 2.50e+03 ... (remaining 3758 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 99 2.60 - 3.18: 17971 3.18 - 3.75: 32459 3.75 - 4.33: 41721 4.33 - 4.90: 71766 Nonbonded interactions: 164016 Sorted by model distance: nonbonded pdb=" OG1 THR C 253 " pdb="MG MG C 602 " model vdw 2.030 2.170 nonbonded pdb=" OG SER C 218 " pdb="MG MG C 602 " model vdw 2.064 2.170 nonbonded pdb=" O ASN B 561 " pdb=" ND2 ASN B 561 " model vdw 2.074 2.520 nonbonded pdb=" OE1 GLN A1126 " pdb=" OH TYR A1194 " model vdw 2.100 2.440 nonbonded pdb=" OH TYR A 669 " pdb=" OE1 GLU A 737 " model vdw 2.208 2.440 ... (remaining 164011 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=0.00 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.220 Check model and map are aligned: 0.300 Set scattering table: 0.210 Process input model: 63.210 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 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 0.101 21971 Z= 0.358 Angle : 0.831 16.645 29981 Z= 0.504 Chirality : 0.148 4.949 3614 Planarity : 0.007 0.160 3761 Dihedral : 13.917 173.191 7462 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.03 % Favored : 96.86 % Rotamer: Outliers : 0.20 % Allowed : 0.66 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.17), residues: 2677 helix: 2.32 (0.14), residues: 1497 sheet: -0.35 (0.36), residues: 198 loop : -1.20 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 766 HIS 0.017 0.001 HIS B 752 PHE 0.038 0.002 PHE B 911 TYR 0.103 0.003 TYR B 777 ARG 0.011 0.000 ARG B 955 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 326 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1950 MET cc_start: 0.6328 (tmm) cc_final: 0.6121 (ppp) REVERT: B 804 THR cc_start: 0.1647 (OUTLIER) cc_final: 0.1156 (m) REVERT: B 860 MET cc_start: 0.2233 (mmt) cc_final: 0.1123 (mmt) outliers start: 4 outliers final: 1 residues processed: 330 average time/residue: 0.3232 time to fit residues: 168.3369 Evaluate side-chains 168 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 955 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 30.0000 chunk 223 optimal weight: 10.0000 chunk 124 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 231 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 267 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1344 GLN A1550 GLN A1854 HIS A2337 HIS A2401 HIS B 498 ASN C 297 HIS C 484 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21971 Z= 0.263 Angle : 0.642 12.948 29981 Z= 0.304 Chirality : 0.041 0.295 3614 Planarity : 0.005 0.090 3761 Dihedral : 8.258 117.367 3216 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.54 % Favored : 97.42 % Rotamer: Outliers : 1.92 % Allowed : 9.02 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.13 (0.17), residues: 2677 helix: 1.98 (0.14), residues: 1507 sheet: -0.22 (0.36), residues: 199 loop : -1.04 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 952 HIS 0.012 0.001 HIS B 575 PHE 0.035 0.002 PHE A1599 TYR 0.020 0.002 TYR A1230 ARG 0.007 0.001 ARG A 743 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1950 MET cc_start: 0.6423 (tmm) cc_final: 0.6142 (ppp) REVERT: B 750 MET cc_start: -0.2868 (ttt) cc_final: -0.3604 (tpt) REVERT: B 860 MET cc_start: 0.2300 (mmt) cc_final: 0.1910 (mmt) outliers start: 38 outliers final: 19 residues processed: 184 average time/residue: 0.2959 time to fit residues: 90.7059 Evaluate side-chains 152 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1488 THR Chi-restraints excluded: chain A residue 1550 GLN Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2344 ASP Chi-restraints excluded: chain A residue 3620 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 222 optimal weight: 0.0770 chunk 182 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 268 optimal weight: 0.8980 chunk 289 optimal weight: 8.9990 chunk 239 optimal weight: 50.0000 chunk 266 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 HIS A1550 GLN A1551 HIS ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21971 Z= 0.144 Angle : 0.489 11.006 29981 Z= 0.232 Chirality : 0.037 0.300 3614 Planarity : 0.004 0.060 3761 Dihedral : 8.275 125.307 3211 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.05 % Favored : 97.91 % Rotamer: Outliers : 1.92 % Allowed : 10.48 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.43 (0.17), residues: 2677 helix: 2.24 (0.14), residues: 1503 sheet: 0.02 (0.37), residues: 198 loop : -0.96 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 798 HIS 0.007 0.001 HIS A1551 PHE 0.021 0.001 PHE A1599 TYR 0.017 0.001 TYR A1185 ARG 0.006 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 2.551 Fit side-chains REVERT: A 1270 MET cc_start: 0.7525 (tpp) cc_final: 0.7258 (mmt) REVERT: A 1950 MET cc_start: 0.6322 (tmm) cc_final: 0.6051 (ppp) REVERT: B 860 MET cc_start: 0.2221 (mmt) cc_final: 0.1477 (mmt) REVERT: B 887 MET cc_start: -0.2420 (mtt) cc_final: -0.3196 (ptt) outliers start: 38 outliers final: 24 residues processed: 163 average time/residue: 0.3000 time to fit residues: 82.4578 Evaluate side-chains 153 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2344 ASP Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 428 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 5.9990 chunk 201 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 285 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 255 optimal weight: 0.4980 chunk 76 optimal weight: 0.1980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 ASN A1550 GLN A2352 HIS B 159 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21971 Z= 0.163 Angle : 0.492 11.350 29981 Z= 0.234 Chirality : 0.037 0.257 3614 Planarity : 0.004 0.057 3761 Dihedral : 8.014 119.526 3211 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 1.92 % Allowed : 12.40 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.43 (0.17), residues: 2677 helix: 2.22 (0.14), residues: 1511 sheet: 0.09 (0.37), residues: 198 loop : -0.95 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 798 HIS 0.008 0.001 HIS B 563 PHE 0.023 0.001 PHE B 580 TYR 0.016 0.001 TYR A1185 ARG 0.005 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 2.573 Fit side-chains REVERT: A 506 LEU cc_start: 0.9376 (mt) cc_final: 0.9031 (tt) REVERT: A 1270 MET cc_start: 0.7546 (tpp) cc_final: 0.7333 (mmt) REVERT: A 1950 MET cc_start: 0.6469 (tmm) cc_final: 0.6176 (ppp) REVERT: B 750 MET cc_start: -0.2452 (ttt) cc_final: -0.3228 (tpt) REVERT: B 860 MET cc_start: 0.2538 (mmt) cc_final: 0.2243 (mmt) REVERT: B 868 MET cc_start: -0.0418 (OUTLIER) cc_final: -0.0731 (ptt) REVERT: B 887 MET cc_start: -0.2381 (mtt) cc_final: -0.3161 (ptt) outliers start: 38 outliers final: 26 residues processed: 160 average time/residue: 0.3068 time to fit residues: 83.8394 Evaluate side-chains 154 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1550 GLN Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2344 ASP Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 2400 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 50.0000 chunk 161 optimal weight: 8.9990 chunk 4 optimal weight: 50.0000 chunk 212 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 145 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 GLN A1258 ASN A2223 GLN A3649 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 21971 Z= 0.348 Angle : 0.636 12.127 29981 Z= 0.313 Chirality : 0.041 0.241 3614 Planarity : 0.005 0.082 3761 Dihedral : 8.358 121.605 3211 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.97 % Rotamer: Outliers : 2.72 % Allowed : 12.50 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.90 (0.17), residues: 2677 helix: 1.73 (0.14), residues: 1499 sheet: -0.23 (0.38), residues: 198 loop : -1.01 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 254 HIS 0.008 0.001 HIS B 575 PHE 0.032 0.002 PHE C 325 TYR 0.021 0.002 TYR A2152 ARG 0.004 0.001 ARG A2374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 115 time to evaluate : 2.750 Fit side-chains revert: symmetry clash REVERT: A 506 LEU cc_start: 0.9462 (mt) cc_final: 0.9167 (tt) REVERT: A 2324 MET cc_start: 0.8703 (tpp) cc_final: 0.8303 (mmm) REVERT: B 750 MET cc_start: -0.2537 (ttt) cc_final: -0.3288 (tpt) REVERT: B 860 MET cc_start: 0.2962 (mmt) cc_final: 0.2665 (mmt) REVERT: B 887 MET cc_start: -0.2437 (mtt) cc_final: -0.3138 (ptt) REVERT: C 328 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8191 (tt) REVERT: C 412 ASN cc_start: 0.8716 (t0) cc_final: 0.8421 (t0) outliers start: 54 outliers final: 36 residues processed: 155 average time/residue: 0.3069 time to fit residues: 80.7523 Evaluate side-chains 145 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1503 MET Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2344 ASP Chi-restraints excluded: chain A residue 2350 VAL Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 285 optimal weight: 2.9990 chunk 236 optimal weight: 40.0000 chunk 132 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1019 ASN A1395 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21971 Z= 0.259 Angle : 0.552 11.879 29981 Z= 0.267 Chirality : 0.038 0.239 3614 Planarity : 0.004 0.058 3761 Dihedral : 8.112 119.144 3211 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 2.67 % Allowed : 13.16 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.17), residues: 2677 helix: 1.88 (0.14), residues: 1501 sheet: -0.25 (0.37), residues: 207 loop : -1.02 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 918 HIS 0.007 0.001 HIS B 575 PHE 0.017 0.001 PHE A1599 TYR 0.015 0.001 TYR A1402 ARG 0.003 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 110 time to evaluate : 2.676 Fit side-chains revert: symmetry clash REVERT: A 506 LEU cc_start: 0.9459 (mt) cc_final: 0.9122 (tt) REVERT: A 849 MET cc_start: 0.8130 (ttp) cc_final: 0.7915 (mtp) REVERT: A 2324 MET cc_start: 0.8680 (tpp) cc_final: 0.8287 (mmm) REVERT: B 219 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7156 (p90) REVERT: B 750 MET cc_start: -0.2618 (ttt) cc_final: -0.3675 (tpt) REVERT: B 860 MET cc_start: 0.3035 (mmt) cc_final: 0.2290 (mmt) REVERT: B 887 MET cc_start: -0.2354 (mtt) cc_final: -0.3069 (ptt) REVERT: C 412 ASN cc_start: 0.8766 (t0) cc_final: 0.8444 (t0) outliers start: 53 outliers final: 37 residues processed: 153 average time/residue: 0.2997 time to fit residues: 78.1022 Evaluate side-chains 142 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 104 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1324 LEU Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1395 GLN Chi-restraints excluded: chain A residue 1503 MET Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2344 ASP Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 502 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 162 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 240 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 173 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1258 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21971 Z= 0.221 Angle : 0.535 12.824 29981 Z= 0.255 Chirality : 0.038 0.242 3614 Planarity : 0.004 0.058 3761 Dihedral : 7.957 118.873 3211 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 2.67 % Allowed : 13.41 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.15 (0.17), residues: 2677 helix: 1.97 (0.14), residues: 1502 sheet: -0.22 (0.36), residues: 207 loop : -0.98 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 798 HIS 0.006 0.001 HIS C 388 PHE 0.017 0.001 PHE A1599 TYR 0.019 0.001 TYR A1125 ARG 0.003 0.000 ARG B 955 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 113 time to evaluate : 2.622 Fit side-chains revert: symmetry clash REVERT: A 506 LEU cc_start: 0.9449 (mt) cc_final: 0.9205 (tt) REVERT: A 849 MET cc_start: 0.8112 (ttp) cc_final: 0.7858 (mtp) REVERT: A 1395 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: B 750 MET cc_start: -0.2523 (ttt) cc_final: -0.3791 (tpt) REVERT: B 887 MET cc_start: -0.2258 (mtt) cc_final: -0.2939 (ptp) REVERT: C 412 ASN cc_start: 0.8816 (t0) cc_final: 0.8474 (t0) outliers start: 53 outliers final: 39 residues processed: 148 average time/residue: 0.2976 time to fit residues: 75.2758 Evaluate side-chains 144 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 104 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1058 MET Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1395 GLN Chi-restraints excluded: chain A residue 1503 MET Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2344 ASP Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 0.2980 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 180 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 223 optimal weight: 0.9980 chunk 258 optimal weight: 0.0020 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21971 Z= 0.130 Angle : 0.506 15.007 29981 Z= 0.237 Chirality : 0.036 0.252 3614 Planarity : 0.004 0.053 3761 Dihedral : 7.721 117.594 3211 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.61 % Favored : 97.35 % Rotamer: Outliers : 1.36 % Allowed : 14.97 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.40 (0.17), residues: 2677 helix: 2.18 (0.14), residues: 1509 sheet: -0.06 (0.37), residues: 201 loop : -0.89 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1629 HIS 0.006 0.001 HIS C 388 PHE 0.018 0.001 PHE A2392 TYR 0.022 0.001 TYR A1125 ARG 0.002 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 506 LEU cc_start: 0.9425 (mt) cc_final: 0.9170 (tt) REVERT: A 849 MET cc_start: 0.8061 (ttp) cc_final: 0.7845 (mtp) REVERT: B 750 MET cc_start: -0.2493 (ttt) cc_final: -0.3780 (tpt) REVERT: B 887 MET cc_start: -0.2145 (mtt) cc_final: -0.2839 (ptp) REVERT: C 247 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 412 ASN cc_start: 0.8769 (t0) cc_final: 0.8427 (t0) outliers start: 27 outliers final: 18 residues processed: 135 average time/residue: 0.2888 time to fit residues: 66.9696 Evaluate side-chains 128 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 502 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 0.0020 chunk 248 optimal weight: 0.8980 chunk 264 optimal weight: 0.0570 chunk 159 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 250 optimal weight: 50.0000 chunk 173 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 overall best weight: 0.9708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2352 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21971 Z= 0.151 Angle : 0.506 13.644 29981 Z= 0.238 Chirality : 0.037 0.252 3614 Planarity : 0.004 0.053 3761 Dihedral : 7.607 116.772 3211 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 1.56 % Allowed : 14.92 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.46 (0.17), residues: 2677 helix: 2.22 (0.14), residues: 1510 sheet: -0.09 (0.36), residues: 207 loop : -0.85 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 798 HIS 0.007 0.001 HIS C 388 PHE 0.016 0.001 PHE A1599 TYR 0.021 0.001 TYR A1125 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 2.672 Fit side-chains revert: symmetry clash REVERT: A 506 LEU cc_start: 0.9435 (mt) cc_final: 0.9186 (tt) REVERT: B 750 MET cc_start: -0.2545 (ttt) cc_final: -0.3831 (tpt) REVERT: B 887 MET cc_start: -0.2200 (mtt) cc_final: -0.2863 (ptt) REVERT: C 247 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7439 (mt-10) REVERT: C 408 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7521 (ptp) REVERT: C 412 ASN cc_start: 0.8764 (t0) cc_final: 0.8375 (t0) outliers start: 31 outliers final: 25 residues processed: 137 average time/residue: 0.3362 time to fit residues: 79.3821 Evaluate side-chains 136 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 502 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 270 optimal weight: 0.5980 chunk 234 optimal weight: 50.0000 chunk 24 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 185 optimal weight: 0.0570 chunk 249 optimal weight: 40.0000 overall best weight: 1.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21971 Z= 0.210 Angle : 0.530 13.834 29981 Z= 0.252 Chirality : 0.037 0.252 3614 Planarity : 0.004 0.054 3761 Dihedral : 7.595 115.710 3211 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 1.51 % Allowed : 14.87 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.41 (0.17), residues: 2677 helix: 2.16 (0.14), residues: 1511 sheet: -0.05 (0.36), residues: 203 loop : -0.85 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 918 HIS 0.005 0.001 HIS B 575 PHE 0.017 0.001 PHE A1599 TYR 0.021 0.001 TYR A1125 ARG 0.005 0.000 ARG C 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 2.804 Fit side-chains revert: symmetry clash REVERT: A 506 LEU cc_start: 0.9446 (mt) cc_final: 0.9216 (tt) REVERT: B 195 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7593 (tt) REVERT: B 750 MET cc_start: -0.2520 (ttt) cc_final: -0.3810 (tpt) REVERT: B 887 MET cc_start: -0.2175 (mtt) cc_final: -0.2815 (ptp) REVERT: C 247 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7448 (mt-10) REVERT: C 408 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7761 (ptp) REVERT: C 412 ASN cc_start: 0.8823 (t0) cc_final: 0.8451 (t0) outliers start: 30 outliers final: 25 residues processed: 130 average time/residue: 0.2908 time to fit residues: 64.3736 Evaluate side-chains 133 residues out of total 2464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 2400 LEU Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 502 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 234 optimal weight: 50.0000 chunk 98 optimal weight: 0.7980 chunk 240 optimal weight: 40.0000 chunk 29 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 13 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: A1395 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.091274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.062011 restraints weight = 70605.444| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.96 r_work: 0.3111 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21971 Z= 0.137 Angle : 0.507 13.728 29981 Z= 0.238 Chirality : 0.036 0.256 3614 Planarity : 0.004 0.052 3761 Dihedral : 7.437 114.120 3211 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.69 % Favored : 97.27 % Rotamer: Outliers : 1.61 % Allowed : 14.82 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.53 (0.17), residues: 2677 helix: 2.27 (0.14), residues: 1503 sheet: 0.13 (0.37), residues: 197 loop : -0.84 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP B 952 HIS 0.007 0.001 HIS C 388 PHE 0.016 0.001 PHE A1599 TYR 0.024 0.001 TYR A1125 ARG 0.003 0.000 ARG B 955 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4607.31 seconds wall clock time: 84 minutes 6.03 seconds (5046.03 seconds total)