Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 01:29:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/04_2023/7pw8_13678_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/04_2023/7pw8_13678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/04_2023/7pw8_13678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/04_2023/7pw8_13678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/04_2023/7pw8_13678_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/04_2023/7pw8_13678_updated.pdb" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.159 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 1 5.21 5 S 93 5.16 5 C 12179 2.51 5 N 3357 2.21 5 O 3318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 864": "OD1" <-> "OD2" Residue "A TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A PHE 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1053": "OD1" <-> "OD2" Residue "A GLU 1082": "OE1" <-> "OE2" Residue "A GLU 1124": "OE1" <-> "OE2" Residue "A GLU 1127": "OE1" <-> "OE2" Residue "A GLU 1361": "OE1" <-> "OE2" Residue "A TYR 2152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2299": "OE1" <-> "OE2" Residue "A ASP 2308": "OD1" <-> "OD2" Residue "A TYR 3654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 203": "OD1" <-> "OD2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18960 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1943, 13720 Classifications: {'peptide': 1943} Incomplete info: {'truncation_to_alanine': 541} Link IDs: {'PTRANS': 61, 'TRANS': 1881} Chain breaks: 39 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1529 Unresolved non-hydrogen angles: 2008 Unresolved non-hydrogen dihedrals: 1109 Unresolved non-hydrogen chiralities: 67 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': 49, 'PHE:plan': 6, 'GLU:plan': 70, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 918 Chain: "B" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2718 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 19, 'TRANS': 356} Chain breaks: 8 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: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2423 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 17, 'TRANS': 292} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 2 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: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ANP': 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} Time building chain proxies: 9.52, per 1000 atoms: 0.50 Number of scatterers: 18960 At special positions: 0 Unit cell: (130.234, 123.424, 178.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 93 16.00 P 12 15.00 Mg 1 11.99 O 3318 8.00 N 3357 7.00 C 12179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.99 Conformation dependent library (CDL) restraints added in 2.8 seconds 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 130 helices and 5 sheets defined 66.8% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.900A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.928A pdb=" N UNK A 172 " --> pdb=" O UNK A 168 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N UNK A 173 " --> pdb=" O UNK A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 removed outlier: 4.970A pdb=" N UNK A 199 " --> pdb=" O UNK A 195 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N UNK A 200 " --> pdb=" O UNK A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 removed outlier: 4.302A pdb=" N UNK A 220 " --> pdb=" O UNK A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.558A 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 282 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.088A pdb=" N UNK A 303 " --> pdb=" O UNK A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 removed outlier: 3.932A pdb=" N THR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 356 through 375 removed outlier: 3.778A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 375 " --> pdb=" O TYR A 371 " (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 475 through 488 removed outlier: 3.707A pdb=" N ASN A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.681A pdb=" N SER A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 523 Processing helix chain 'A' and resid 529 through 535 removed outlier: 3.938A pdb=" N ARG A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TYR A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 554 Processing helix chain 'A' and resid 558 through 583 removed outlier: 4.069A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) 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: 3.693A pdb=" N ILE A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 Processing helix chain 'A' and resid 647 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: 3.767A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS A 675 " --> pdb=" O HIS A 671 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 676 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N HIS A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE A 678 " --> pdb=" O ARG A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 725 through 743 removed outlier: 3.733A pdb=" N ARG A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Proline residue: A 750 - end of helix removed outlier: 3.786A pdb=" N SER A 753 " --> pdb=" O PRO A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 766 Processing helix chain 'A' and resid 773 through 785 Processing helix chain 'A' and resid 792 through 805 removed outlier: 3.693A pdb=" N ARG A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 800 " --> pdb=" O GLN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.504A pdb=" N SER A 823 " --> pdb=" O LYS A 819 " (cutoff:3.500A) 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 removed outlier: 3.531A pdb=" N GLU A 840 " --> pdb=" O THR A 836 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 842 " --> pdb=" O ILE A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 870 Processing helix chain 'A' and resid 882 through 890 Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 909 through 926 Processing helix chain 'A' and resid 936 through 955 removed outlier: 3.687A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 998 removed outlier: 4.049A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 Processing helix chain 'A' and resid 1020 through 1040 removed outlier: 4.700A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1057 Processing helix chain 'A' and resid 1068 through 1082 removed outlier: 3.500A pdb=" N THR A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1098 removed outlier: 3.855A pdb=" N SER A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1115 removed outlier: 3.554A pdb=" N GLU A1115 " --> pdb=" O ALA A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1133 removed outlier: 3.738A pdb=" N VAL A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1150 removed outlier: 3.954A pdb=" N LEU A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1196 Processing helix chain 'A' and resid 1200 through 1215 Processing helix chain 'A' and resid 1228 through 1239 Processing helix chain 'A' and resid 1242 through 1249 Processing helix chain 'A' and resid 1282 through 1304 Processing helix chain 'A' and resid 1318 through 1331 removed outlier: 3.955A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1340 removed outlier: 3.764A pdb=" N THR A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1340 " --> pdb=" O ARG A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1366 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: 3.697A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A1403 " --> pdb=" O TYR A1399 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS A1409 " --> pdb=" O GLN A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1435 removed outlier: 3.540A 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 Processing helix chain 'A' and resid 1480 through 1494 Processing helix chain 'A' and resid 1497 through 1513 removed outlier: 3.885A pdb=" N LYS A1513 " --> pdb=" O ILE A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1534 removed outlier: 4.157A pdb=" N ALA A1522 " --> pdb=" O GLU A1518 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A1534 " --> pdb=" O LYS A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1550 removed outlier: 5.135A pdb=" N GLY A1541 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLN A1542 " --> pdb=" O GLU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1560 through 1569 Processing helix chain 'A' and resid 1596 through 1611 removed outlier: 4.035A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 3.865A 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: 3.749A pdb=" N UNK A1674 " --> pdb=" O UNK A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1715 Processing helix chain 'A' and resid 1729 through 1758 removed outlier: 3.735A pdb=" N SER A1742 " --> pdb=" O ASP A1738 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU A1743 " --> pdb=" O ARG A1739 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR A1744 " --> pdb=" O ILE A1740 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A1758 " --> pdb=" O PHE A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1798 Processing helix chain 'A' and resid 1804 through 1813 removed outlier: 3.909A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1831 removed outlier: 3.692A pdb=" N LEU A1830 " --> pdb=" O LEU A1826 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASN A1831 " --> pdb=" O PHE A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1849 Processing helix chain 'A' and resid 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' Processing helix chain 'A' and resid 1857 through 1864 Processing helix chain 'A' and resid 1924 through 1939 removed outlier: 4.066A pdb=" N ASP A1928 " --> pdb=" O MET A1925 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N CYS A1929 " --> 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 2019 Processing helix chain 'A' and resid 2036 through 2055 removed outlier: 6.913A pdb=" N ASP A2046 " --> pdb=" O ASP A2042 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA A2047 " --> pdb=" O ASN A2043 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE A2048 " --> pdb=" O TYR A2044 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU A2049 " --> pdb=" O GLY A2045 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2082 Processing helix chain 'A' and resid 2161 through 2177 removed outlier: 3.688A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A2176 " --> pdb=" O ILE A2172 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE A2177 " --> pdb=" O VAL A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2180 through 2182 No H-bonds generated for 'chain 'A' and resid 2180 through 2182' Processing helix chain 'A' and resid 2214 through 2231 removed outlier: 3.595A pdb=" N GLN A2231 " --> pdb=" O LEU A2228 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2262 removed outlier: 3.661A 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 2290 removed outlier: 3.607A pdb=" N ALA A2290 " --> pdb=" O GLU A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2303 Processing helix chain 'A' and resid 2307 through 2331 Processing helix chain 'A' and resid 2361 through 2363 No H-bonds generated for 'chain 'A' and resid 2361 through 2363' Processing helix chain 'A' and resid 2377 through 2383 removed outlier: 3.507A pdb=" N ALA A2382 " --> pdb=" O ASN A2378 " (cutoff:3.500A) removed outlier: 4.062A 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 3620 Processing helix chain 'A' and resid 3633 through 3645 Processing helix chain 'A' and resid 3647 through 3651 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 7 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 71 Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.683A pdb=" N ARG B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 205 removed outlier: 3.878A pdb=" N HIS B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 234 removed outlier: 3.672A pdb=" N PHE B 227 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 231 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 232 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 296 through 314 Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'B' and resid 410 through 422 removed outlier: 4.373A pdb=" N HIS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 457 removed outlier: 3.672A pdb=" N ALA B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 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 558 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 248 removed outlier: 3.844A pdb=" N GLU C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 248' Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 296 through 314 Processing helix chain 'C' and resid 330 through 340 removed outlier: 3.600A pdb=" N VAL C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 381 through 394 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 466 through 479 removed outlier: 3.682A pdb=" N SER C 479 " --> pdb=" O SER C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 507 removed outlier: 3.791A pdb=" N PHE C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS C 497 " --> pdb=" O LYS C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 Processing sheet with id= A, first strand: chain 'A' and resid 2129 through 2131 removed outlier: 3.710A pdb=" N THR A2129 " --> pdb=" O LYS A2139 " (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 'A' and resid 2121 through 2124 removed outlier: 6.464A pdb=" N LEU A2143 " --> pdb=" O HIS A2122 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 336 through 339 removed outlier: 8.769A pdb=" N TYR B 337 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 267 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL B 339 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE B 269 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 270 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY B 54 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 148 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 428 through 432 removed outlier: 8.616A pdb=" N PHE C 429 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE C 369 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL C 431 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN C 371 " --> pdb=" O VAL C 431 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 317 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 209 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR C 270 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY C 211 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 256 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE C 258 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LYS C 182 " --> pdb=" O PHE C 258 " (cutoff:3.500A) 1071 hydrogen bonds defined for protein. 3093 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: 7.94 Time building geometry restraints manager: 8.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 15 1.21 - 1.36: 6186 1.36 - 1.51: 5220 1.51 - 1.66: 7742 1.66 - 1.81: 142 Bond restraints: 19305 Sorted by residual: bond pdb=" C ILE A 838 " pdb=" O ILE A 838 " ideal model delta sigma weight residual 1.237 1.068 0.169 1.19e-02 7.06e+03 2.03e+02 bond pdb=" C LEU A 830 " pdb=" O LEU A 830 " ideal model delta sigma weight residual 1.235 1.058 0.177 1.32e-02 5.74e+03 1.80e+02 bond pdb=" C HIS A 835 " pdb=" O HIS A 835 " ideal model delta sigma weight residual 1.234 1.082 0.152 1.19e-02 7.06e+03 1.63e+02 bond pdb=" CE1 HIS A 835 " pdb=" NE2 HIS A 835 " ideal model delta sigma weight residual 1.321 1.194 0.127 1.00e-02 1.00e+04 1.62e+02 bond pdb=" C GLN A 839 " pdb=" O GLN A 839 " ideal model delta sigma weight residual 1.236 1.078 0.159 1.26e-02 6.30e+03 1.59e+02 ... (remaining 19300 not shown) Histogram of bond angle deviations from ideal: 99.55 - 107.58: 747 107.58 - 115.60: 11919 115.60 - 123.63: 13161 123.63 - 131.65: 494 131.65 - 139.68: 46 Bond angle restraints: 26367 Sorted by residual: angle pdb=" CA HIS A 835 " pdb=" CB HIS A 835 " pdb=" CG HIS A 835 " ideal model delta sigma weight residual 113.80 121.00 -7.20 1.00e+00 1.00e+00 5.18e+01 angle pdb=" CA ASN A 833 " pdb=" CB ASN A 833 " pdb=" CG ASN A 833 " ideal model delta sigma weight residual 112.60 106.08 6.52 1.00e+00 1.00e+00 4.25e+01 angle pdb=" C ASN A 834 " pdb=" CA ASN A 834 " pdb=" CB ASN A 834 " ideal model delta sigma weight residual 109.51 120.49 -10.98 1.71e+00 3.42e-01 4.12e+01 angle pdb=" N THR C 326 " pdb=" CA THR C 326 " pdb=" C THR C 326 " ideal model delta sigma weight residual 110.91 118.36 -7.45 1.17e+00 7.31e-01 4.05e+01 angle pdb=" C GLN A 839 " pdb=" N GLU A 840 " pdb=" CA GLU A 840 " ideal model delta sigma weight residual 120.28 128.53 -8.25 1.34e+00 5.57e-01 3.79e+01 ... (remaining 26362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 10880 21.65 - 43.30: 472 43.30 - 64.96: 50 64.96 - 86.61: 19 86.61 - 108.26: 2 Dihedral angle restraints: 11423 sinusoidal: 3702 harmonic: 7721 Sorted by residual: dihedral pdb=" C ASN A 834 " pdb=" N ASN A 834 " pdb=" CA ASN A 834 " pdb=" CB ASN A 834 " ideal model delta harmonic sigma weight residual -122.60 -145.53 22.93 0 2.50e+00 1.60e-01 8.41e+01 dihedral pdb=" N ASN A 834 " pdb=" C ASN A 834 " pdb=" CA ASN A 834 " pdb=" CB ASN A 834 " ideal model delta harmonic sigma weight residual 122.80 144.05 -21.25 0 2.50e+00 1.60e-01 7.23e+01 dihedral pdb=" N ASN A 832 " pdb=" C ASN A 832 " pdb=" CA ASN A 832 " pdb=" CB ASN A 832 " ideal model delta harmonic sigma weight residual 122.80 139.94 -17.14 0 2.50e+00 1.60e-01 4.70e+01 ... (remaining 11420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.006: 3244 1.006 - 2.012: 0 2.012 - 3.019: 0 3.019 - 4.025: 0 4.025 - 5.031: 3 Chirality restraints: 3247 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 2.51 -5.03 2.00e-01 2.50e+01 6.33e+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 -2.36 4.84 2.00e-01 2.50e+01 5.86e+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 -2.49 4.80 2.00e-01 2.50e+01 5.77e+02 ... (remaining 3244 not shown) Planarity restraints: 3274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 836 " 0.022 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C THR A 836 " -0.079 2.00e-02 2.50e+03 pdb=" O THR A 836 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU A 837 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 839 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C GLN A 839 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 839 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 840 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 833 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" CG ASN A 833 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 833 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 833 " -0.011 2.00e-02 2.50e+03 ... (remaining 3271 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 122 2.65 - 3.21: 17107 3.21 - 3.77: 28402 3.77 - 4.34: 37690 4.34 - 4.90: 63372 Nonbonded interactions: 146693 Sorted by model distance: nonbonded pdb=" OG SER C 218 " pdb="MG MG C 602 " model vdw 2.086 2.170 nonbonded pdb=" OG1 THR C 253 " pdb="MG MG C 602 " model vdw 2.128 2.170 nonbonded pdb=" O SER A 616 " pdb=" OG1 THR A 619 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR A2193 " pdb=" O ILE A2353 " model vdw 2.233 2.440 nonbonded pdb=" O1G ANP A3702 " pdb=" O2B ANP A3702 " model vdw 2.239 3.040 ... (remaining 146688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.270 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 49.690 Find NCS groups from input model: 0.610 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:14.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 0.177 19305 Z= 0.336 Angle : 0.749 16.767 26367 Z= 0.433 Chirality : 0.156 5.031 3247 Planarity : 0.004 0.046 3274 Dihedral : 12.384 108.262 6349 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2354 helix: 1.87 (0.14), residues: 1493 sheet: 0.19 (0.43), residues: 129 loop : -1.38 (0.23), residues: 732 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 288 time to evaluate : 2.229 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 291 average time/residue: 1.3784 time to fit residues: 449.5032 Evaluate side-chains 195 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 9.9990 chunk 198 optimal weight: 0.0870 chunk 110 optimal weight: 0.0370 chunk 67 optimal weight: 0.0970 chunk 133 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 152 optimal weight: 0.0060 chunk 237 optimal weight: 0.0270 overall best weight: 0.0508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 600 HIS A 833 ASN A 881 ASN A1276 ASN A1344 GLN A1854 HIS A1947 GLN A2206 GLN A2278 HIS A2352 HIS B 159 ASN B 416 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 19305 Z= 0.122 Angle : 0.455 11.327 26367 Z= 0.222 Chirality : 0.036 0.378 3247 Planarity : 0.004 0.038 3274 Dihedral : 3.870 106.812 2761 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.18), residues: 2354 helix: 2.17 (0.14), residues: 1502 sheet: 0.69 (0.43), residues: 129 loop : -1.26 (0.23), residues: 723 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 2.105 Fit side-chains outliers start: 23 outliers final: 7 residues processed: 225 average time/residue: 1.2912 time to fit residues: 330.3804 Evaluate side-chains 200 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 2.287 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.5737 time to fit residues: 6.7383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 30.0000 chunk 73 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 236 optimal weight: 0.0870 chunk 81 optimal weight: 0.8980 chunk 191 optimal weight: 0.2980 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 881 ASN A1854 HIS A2278 HIS A2356 ASN B 208 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 19305 Z= 0.161 Angle : 0.471 9.429 26367 Z= 0.235 Chirality : 0.037 0.269 3247 Planarity : 0.004 0.039 3274 Dihedral : 4.119 106.710 2761 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2354 helix: 2.15 (0.14), residues: 1514 sheet: 0.76 (0.42), residues: 129 loop : -1.24 (0.23), residues: 711 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 2.357 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 206 average time/residue: 1.3532 time to fit residues: 315.5841 Evaluate side-chains 198 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 2.196 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 5 average time/residue: 0.2382 time to fit residues: 4.9681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 123 optimal weight: 0.0470 chunk 26 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1533 GLN A1854 HIS A2278 HIS A2352 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8319 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 19305 Z= 0.185 Angle : 0.477 9.518 26367 Z= 0.239 Chirality : 0.037 0.261 3247 Planarity : 0.004 0.042 3274 Dihedral : 4.367 108.110 2761 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2354 helix: 2.08 (0.14), residues: 1516 sheet: 0.82 (0.43), residues: 129 loop : -1.25 (0.23), residues: 709 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 185 time to evaluate : 2.076 Fit side-chains outliers start: 40 outliers final: 22 residues processed: 212 average time/residue: 1.2390 time to fit residues: 300.7091 Evaluate side-chains 201 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 15 residues processed: 7 average time/residue: 0.7247 time to fit residues: 9.2019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 188 optimal weight: 0.0050 chunk 104 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 129 optimal weight: 0.1980 chunk 227 optimal weight: 40.0000 chunk 63 optimal weight: 0.3980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 725 GLN A 881 ASN A1533 GLN A1854 HIS A2278 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 19305 Z= 0.119 Angle : 0.419 8.375 26367 Z= 0.210 Chirality : 0.035 0.269 3247 Planarity : 0.003 0.040 3274 Dihedral : 4.093 102.224 2761 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.18), residues: 2354 helix: 2.28 (0.14), residues: 1518 sheet: 0.96 (0.43), residues: 129 loop : -1.20 (0.23), residues: 707 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 2.163 Fit side-chains outliers start: 32 outliers final: 20 residues processed: 199 average time/residue: 1.3060 time to fit residues: 296.8332 Evaluate side-chains 193 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 2.045 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.2323 time to fit residues: 3.9903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 0.6980 chunk 228 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 253 optimal weight: 0.0270 chunk 210 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 133 optimal weight: 30.0000 overall best weight: 1.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1533 GLN A1854 HIS A2278 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8353 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 19305 Z= 0.243 Angle : 0.515 8.672 26367 Z= 0.258 Chirality : 0.039 0.288 3247 Planarity : 0.004 0.046 3274 Dihedral : 4.503 108.686 2761 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2354 helix: 2.02 (0.14), residues: 1516 sheet: 0.94 (0.43), residues: 129 loop : -1.26 (0.22), residues: 709 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 2.171 Fit side-chains outliers start: 39 outliers final: 24 residues processed: 206 average time/residue: 1.3859 time to fit residues: 321.7709 Evaluate side-chains 198 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 174 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 5 average time/residue: 0.2187 time to fit residues: 4.8248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 0.5980 chunk 28 optimal weight: 0.0770 chunk 144 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 141 optimal weight: 0.0870 chunk 252 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1204 GLN A1533 GLN A1854 HIS A2278 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8285 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 19305 Z= 0.120 Angle : 0.424 7.172 26367 Z= 0.212 Chirality : 0.035 0.266 3247 Planarity : 0.003 0.042 3274 Dihedral : 4.175 102.642 2761 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.18), residues: 2354 helix: 2.30 (0.14), residues: 1513 sheet: 0.98 (0.43), residues: 129 loop : -1.21 (0.23), residues: 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 178 time to evaluate : 2.165 Fit side-chains outliers start: 33 outliers final: 23 residues processed: 200 average time/residue: 1.3076 time to fit residues: 298.0624 Evaluate side-chains 198 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 2.146 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.6032 time to fit residues: 6.0167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 124 optimal weight: 0.0270 chunk 23 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1533 GLN A1854 HIS A2278 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8289 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 19305 Z= 0.129 Angle : 0.427 7.537 26367 Z= 0.213 Chirality : 0.035 0.240 3247 Planarity : 0.003 0.042 3274 Dihedral : 4.018 97.663 2761 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.18), residues: 2354 helix: 2.35 (0.14), residues: 1520 sheet: 1.01 (0.43), residues: 129 loop : -1.17 (0.23), residues: 705 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 2.101 Fit side-chains outliers start: 32 outliers final: 23 residues processed: 202 average time/residue: 1.4137 time to fit residues: 322.9983 Evaluate side-chains 197 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 2.247 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.5935 time to fit residues: 6.8879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 8.9990 chunk 241 optimal weight: 0.7980 chunk 220 optimal weight: 0.9990 chunk 235 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 212 optimal weight: 0.3980 chunk 222 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1533 GLN A1854 HIS A2278 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8285 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 19305 Z= 0.130 Angle : 0.430 7.789 26367 Z= 0.214 Chirality : 0.035 0.233 3247 Planarity : 0.003 0.042 3274 Dihedral : 3.925 90.974 2761 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.18), residues: 2354 helix: 2.37 (0.14), residues: 1519 sheet: 1.02 (0.43), residues: 129 loop : -1.16 (0.23), residues: 706 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 2.088 Fit side-chains outliers start: 23 outliers final: 20 residues processed: 197 average time/residue: 1.3837 time to fit residues: 308.7770 Evaluate side-chains 191 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 2.222 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.2367 time to fit residues: 3.8238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 151 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 chunk 172 optimal weight: 0.0010 chunk 261 optimal weight: 10.0000 chunk 240 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1533 GLN A1854 HIS A2278 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8309 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 19305 Z= 0.153 Angle : 0.453 8.017 26367 Z= 0.225 Chirality : 0.036 0.237 3247 Planarity : 0.004 0.043 3274 Dihedral : 3.953 86.192 2761 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.18), residues: 2354 helix: 2.29 (0.14), residues: 1522 sheet: 1.02 (0.43), residues: 129 loop : -1.16 (0.23), residues: 703 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 2.146 Fit side-chains outliers start: 25 outliers final: 22 residues processed: 191 average time/residue: 1.3139 time to fit residues: 284.8803 Evaluate side-chains 194 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 2.180 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.5828 time to fit residues: 5.9418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 208 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1533 GLN A1854 HIS A2278 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.117815 restraints weight = 22241.255| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.05 r_work: 0.3010 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 19305 Z= 0.245 Angle : 0.526 8.970 26367 Z= 0.263 Chirality : 0.039 0.241 3247 Planarity : 0.004 0.044 3274 Dihedral : 4.256 83.965 2761 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2354 helix: 2.03 (0.14), residues: 1524 sheet: 0.99 (0.43), residues: 129 loop : -1.27 (0.22), residues: 701 =============================================================================== Job complete usr+sys time: 5895.37 seconds wall clock time: 105 minutes 31.68 seconds (6331.68 seconds total)