Starting phenix.real_space_refine on Sat Jul 4 06:59:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pfr_71611/07_2026/9pfr_71611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pfr_71611/07_2026/9pfr_71611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pfr_71611/07_2026/9pfr_71611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pfr_71611/07_2026/9pfr_71611.map" model { file = "/net/cci-nas-00/data/ceres_data/9pfr_71611/07_2026/9pfr_71611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pfr_71611/07_2026/9pfr_71611.cif" } resolution = 3.08 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 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= 0.002 sd= 0.071 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 17 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 11844 2.51 5 N 3124 2.21 5 O 3448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18533 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1959, 16030 Classifications: {'peptide': 1959} Link IDs: {'PTRANS': 62, 'TRANS': 1896} Chain breaks: 7 Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 430 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "D" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 470 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain breaks: 1 Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 839 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 1 Chain: "P" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "T" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 223 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ZAN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.06, per 1000 atoms: 0.22 Number of scatterers: 18533 At special positions: 0 Unit cell: (124.844, 124.844, 104.742, 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 99 16.00 P 17 15.00 Mg 1 11.99 O 3448 8.00 N 3124 7.00 C 11844 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 - 3.00 Amino acid : True - 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: 1.79 Conformation dependent library (CDL) restraints added in 845.1 milliseconds 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4304 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 13 sheets defined 60.6% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.509A pdb=" N CYS A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 4.070A pdb=" N LEU A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 98 through 132 removed outlier: 4.089A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 201 through 228 Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.797A pdb=" N LEU A 295 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 327 through 333 removed outlier: 4.250A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 351 through 379 removed outlier: 4.375A pdb=" N PHE A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 396 through 413 removed outlier: 4.275A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 423 through 426 Processing helix chain 'A' and resid 435 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.865A pdb=" N VAL A 488 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 489 " --> pdb=" O ALA A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 489' Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.674A pdb=" N ILE A 549 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 552 " --> pdb=" O ILE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 596 through 604 Processing helix chain 'A' and resid 633 through 651 Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 663 through 678 removed outlier: 3.654A pdb=" N GLN A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 716 through 725 removed outlier: 3.579A pdb=" N LEU A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 828 through 851 removed outlier: 4.064A pdb=" N LEU A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 849 " --> pdb=" O TYR A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 901 through 920 removed outlier: 4.061A pdb=" N GLU A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 removed outlier: 3.738A pdb=" N HIS A 944 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 992 through 997 Processing helix chain 'A' and resid 1003 through 1021 removed outlier: 4.152A pdb=" N GLU A1007 " --> pdb=" O ASP A1003 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1045 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1087 removed outlier: 4.984A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1111 removed outlier: 4.601A pdb=" N MET A1111 " --> pdb=" O LEU A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1143 removed outlier: 3.828A pdb=" N ALA A1134 " --> pdb=" O PRO A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1153 removed outlier: 3.550A pdb=" N GLU A1152 " --> pdb=" O ASN A1149 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A1153 " --> pdb=" O ILE A1150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1149 through 1153' Processing helix chain 'A' and resid 1159 through 1174 Processing helix chain 'A' and resid 1175 through 1180 Processing helix chain 'A' and resid 1198 through 1212 Processing helix chain 'A' and resid 1223 through 1227 Processing helix chain 'A' and resid 1277 through 1281 removed outlier: 3.572A pdb=" N VAL A1280 " --> pdb=" O ASN A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1325 Processing helix chain 'A' and resid 1354 through 1359 Processing helix chain 'A' and resid 1367 through 1376 removed outlier: 4.248A pdb=" N ILE A1371 " --> pdb=" O PRO A1367 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A1374 " --> pdb=" O ARG A1370 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A1375 " --> pdb=" O ILE A1371 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1404 Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1452 through 1460 removed outlier: 3.676A pdb=" N GLU A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A1460 " --> pdb=" O TYR A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1485 removed outlier: 3.642A pdb=" N ASP A1484 " --> pdb=" O LYS A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1510 removed outlier: 4.095A pdb=" N ILE A1491 " --> pdb=" O HIS A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1522 through 1528 removed outlier: 3.952A pdb=" N PHE A1528 " --> pdb=" O THR A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1546 Processing helix chain 'A' and resid 1564 through 1569 Processing helix chain 'A' and resid 1571 through 1583 removed outlier: 4.002A pdb=" N TRP A1575 " --> pdb=" O ASP A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1592 removed outlier: 3.950A pdb=" N TYR A1590 " --> pdb=" O LYS A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1600 removed outlier: 3.984A pdb=" N LEU A1598 " --> pdb=" O ASP A1595 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS A1599 " --> pdb=" O ALA A1596 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A1600 " --> pdb=" O SER A1597 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1595 through 1600' Processing helix chain 'A' and resid 1603 through 1617 removed outlier: 3.725A pdb=" N VAL A1617 " --> pdb=" O LYS A1613 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1647 Processing helix chain 'A' and resid 1665 through 1671 removed outlier: 3.522A pdb=" N TYR A1669 " --> pdb=" O ASN A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1696 Processing helix chain 'A' and resid 1764 through 1770 Processing helix chain 'A' and resid 1814 through 1818 Processing helix chain 'A' and resid 1833 through 1842 Processing helix chain 'A' and resid 1857 through 1866 Processing helix chain 'A' and resid 1881 through 1886 removed outlier: 3.732A pdb=" N LEU A1886 " --> pdb=" O ASP A1883 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1894 Processing helix chain 'A' and resid 1907 through 1911 Processing helix chain 'A' and resid 1941 through 1958 removed outlier: 3.671A pdb=" N ILE A1948 " --> pdb=" O ASN A1944 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A1949 " --> pdb=" O TRP A1945 " (cutoff:3.500A) Processing helix chain 'A' and resid 2019 through 2034 Processing helix chain 'A' and resid 2043 through 2053 Processing helix chain 'A' and resid 2065 through 2076 removed outlier: 4.279A pdb=" N LEU A2071 " --> pdb=" O ILE A2067 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A2076 " --> pdb=" O SER A2072 " (cutoff:3.500A) Processing helix chain 'A' and resid 2097 through 2116 removed outlier: 3.718A pdb=" N ASN A2115 " --> pdb=" O ASN A2111 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE A2116 " --> pdb=" O HIS A2112 " (cutoff:3.500A) Processing helix chain 'A' and resid 2122 through 2132 Processing helix chain 'A' and resid 2135 through 2143 removed outlier: 3.927A pdb=" N LEU A2143 " --> pdb=" O LEU A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2144 through 2159 Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 157 through 164 removed outlier: 3.882A pdb=" N ALA B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'C' and resid 129 through 156 Processing helix chain 'C' and resid 161 through 183 removed outlier: 3.668A pdb=" N GLY C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 Processing helix chain 'D' and resid 172 through 200 Processing helix chain 'E' and resid 130 through 151 Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 217 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.260A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL A 263 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 253 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.556A pdb=" N VAL A 614 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 691 through 694 Processing sheet with id=AA6, first strand: chain 'A' and resid 813 through 815 removed outlier: 3.905A pdb=" N ILE A 698 " --> pdb=" O TYR A 861 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.664A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1228 through 1233 removed outlier: 3.750A pdb=" N ILE A1243 " --> pdb=" O ILE A1410 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A1241 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1271 through 1272 Processing sheet with id=AB1, first strand: chain 'A' and resid 1625 through 1626 removed outlier: 6.137A pdb=" N TRP A1625 " --> pdb=" O ILE A1676 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1776 through 1778 Processing sheet with id=AB3, first strand: chain 'A' and resid 1900 through 1901 removed outlier: 6.635A pdb=" N CYS A1848 " --> pdb=" O LEU A1932 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N VAL A1934 " --> pdb=" O CYS A1848 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA A1850 " --> pdb=" O VAL A1934 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL A2008 " --> pdb=" O LEU A1990 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A1990 " --> pdb=" O VAL A2008 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A2010 " --> pdb=" O THR A1988 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1974 through 1975 removed outlier: 3.526A pdb=" N TYR A1974 " --> pdb=" O VAL A2005 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2772 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: 4.52 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5703 1.34 - 1.46: 2867 1.46 - 1.58: 10159 1.58 - 1.70: 31 1.70 - 1.82: 161 Bond restraints: 18921 Sorted by residual: bond pdb=" O3B ZAN A2202 " pdb=" PG ZAN A2202 " ideal model delta sigma weight residual 1.740 1.609 0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" N3A ZAN A2202 " pdb=" PB ZAN A2202 " ideal model delta sigma weight residual 1.697 1.610 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C4 ZAN A2202 " pdb=" C5 ZAN A2202 " ideal model delta sigma weight residual 1.386 1.472 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" N3A ZAN A2202 " pdb=" PA ZAN A2202 " ideal model delta sigma weight residual 1.689 1.607 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C5 ZAN A2202 " pdb=" C6 ZAN A2202 " ideal model delta sigma weight residual 1.407 1.477 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 18916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 25341 2.55 - 5.09: 266 5.09 - 7.64: 26 7.64 - 10.19: 10 10.19 - 12.74: 1 Bond angle restraints: 25644 Sorted by residual: angle pdb=" C GLY A 810 " pdb=" N ASP A 811 " pdb=" CA ASP A 811 " ideal model delta sigma weight residual 125.66 133.70 -8.04 1.85e+00 2.92e-01 1.89e+01 angle pdb=" PA ZAN A2202 " pdb=" N3A ZAN A2202 " pdb=" PB ZAN A2202 " ideal model delta sigma weight residual 133.19 120.45 12.74 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C TYR A2006 " pdb=" N LEU A2007 " pdb=" CA LEU A2007 " ideal model delta sigma weight residual 121.24 126.96 -5.72 1.44e+00 4.82e-01 1.58e+01 angle pdb=" N ASN A1944 " pdb=" CA ASN A1944 " pdb=" C ASN A1944 " ideal model delta sigma weight residual 111.28 107.10 4.18 1.09e+00 8.42e-01 1.47e+01 angle pdb=" CA PHE A1771 " pdb=" CB PHE A1771 " pdb=" CG PHE A1771 " ideal model delta sigma weight residual 113.80 117.58 -3.78 1.00e+00 1.00e+00 1.43e+01 ... (remaining 25639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10157 17.96 - 35.91: 1083 35.91 - 53.87: 221 53.87 - 71.82: 43 71.82 - 89.78: 18 Dihedral angle restraints: 11522 sinusoidal: 4889 harmonic: 6633 Sorted by residual: dihedral pdb=" CA GLU A 349 " pdb=" C GLU A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LEU A 499 " pdb=" C LEU A 499 " pdb=" N ASN A 500 " pdb=" CA ASN A 500 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA PRO A1909 " pdb=" C PRO A1909 " pdb=" N ALA A1910 " pdb=" CA ALA A1910 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 11519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2267 0.046 - 0.091: 539 0.091 - 0.137: 136 0.137 - 0.183: 19 0.183 - 0.229: 4 Chirality restraints: 2965 Sorted by residual: chirality pdb=" CA LYS A1659 " pdb=" N LYS A1659 " pdb=" C LYS A1659 " pdb=" CB LYS A1659 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE A1651 " pdb=" CA ILE A1651 " pdb=" CG1 ILE A1651 " pdb=" CG2 ILE A1651 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA PHE A1771 " pdb=" N PHE A1771 " pdb=" C PHE A1771 " pdb=" CB PHE A1771 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2962 not shown) Planarity restraints: 3146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A2038 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO A2039 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO A2039 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A2039 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 480 " -0.024 2.00e-02 2.50e+03 2.66e-02 1.76e+01 pdb=" CG TRP A 480 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP A 480 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 480 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 480 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 480 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 480 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 480 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 480 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 480 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1972 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.04e+00 pdb=" C VAL A1972 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL A1972 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A1973 " 0.013 2.00e-02 2.50e+03 ... (remaining 3143 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 164 2.55 - 3.14: 14314 3.14 - 3.73: 30478 3.73 - 4.31: 42428 4.31 - 4.90: 71218 Nonbonded interactions: 158602 Sorted by model distance: nonbonded pdb="MG MG A2201 " pdb=" O1B ZAN A2202 " model vdw 1.966 2.170 nonbonded pdb=" OD1 ASP A 700 " pdb="MG MG A2201 " model vdw 2.061 2.170 nonbonded pdb=" OD2 ASP A 811 " pdb="MG MG A2201 " model vdw 2.107 2.170 nonbonded pdb=" OD1 ASP A 700 " pdb=" O LEU A 701 " model vdw 2.169 3.040 nonbonded pdb=" OD1 ASP A 121 " pdb=" OG1 THR A 187 " model vdw 2.221 3.040 ... (remaining 158597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 130 through 183) selection = (chain 'C' and resid 130 through 183) } 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=0.20 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: 0.760 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.600 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.003 0.131 18921 Z= 0.184 Angle : 0.654 12.737 25644 Z= 0.358 Chirality : 0.043 0.229 2965 Planarity : 0.004 0.111 3146 Dihedral : 15.346 89.777 7218 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2213 helix: 1.18 (0.14), residues: 1242 sheet: -1.77 (0.46), residues: 105 loop : -1.26 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1000 TYR 0.020 0.001 TYR A1246 PHE 0.035 0.002 PHE A2116 TRP 0.068 0.002 TRP A 480 HIS 0.008 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (18921) covalent geometry : angle 0.65438 / 0.36 (25644) hydrogen bonds : bond 0.12508 / 7.98 ( 953) hydrogen bonds : angle 5.60060 / 4.03 ( 2772) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.672 Fit side-chains REVERT: A 413 ASP cc_start: 0.8740 (t70) cc_final: 0.8365 (t0) REVERT: A 611 ASN cc_start: 0.8206 (p0) cc_final: 0.8004 (p0) REVERT: A 778 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7184 (mt-10) REVERT: A 821 ILE cc_start: 0.8752 (tt) cc_final: 0.8509 (tt) REVERT: A 1044 ILE cc_start: 0.7596 (tt) cc_final: 0.7370 (tt) REVERT: A 1049 ASN cc_start: 0.8087 (t0) cc_final: 0.7758 (t0) REVERT: A 1648 MET cc_start: 0.5869 (ptp) cc_final: 0.5324 (ptp) REVERT: A 1849 ILE cc_start: 0.8545 (mp) cc_final: 0.8220 (mt) REVERT: A 2043 ASP cc_start: 0.8368 (t0) cc_final: 0.8123 (t0) REVERT: B 143 SER cc_start: 0.8694 (t) cc_final: 0.8411 (t) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.1221 time to fit residues: 68.1214 Evaluate side-chains 316 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN A 220 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 640 GLN A 991 ASN ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 GLN A1215 ASN A1417 ASN A1817 HIS ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.160140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124288 restraints weight = 22060.948| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.82 r_work: 0.3301 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18921 Z= 0.123 Angle : 0.510 6.865 25644 Z= 0.270 Chirality : 0.039 0.163 2965 Planarity : 0.004 0.071 3146 Dihedral : 8.049 73.928 2688 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.78 % Allowed : 7.66 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.18), residues: 2213 helix: 1.59 (0.15), residues: 1259 sheet: -1.40 (0.44), residues: 127 loop : -1.06 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1000 TYR 0.021 0.001 TYR A1226 PHE 0.025 0.001 PHE A2116 TRP 0.024 0.001 TRP A 480 HIS 0.009 0.001 HIS A1918 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (18921) covalent geometry : angle 0.51036 / 0.27 (25644) hydrogen bonds : bond 0.03762 / 2.46 ( 953) hydrogen bonds : angle 4.61614 / 3.31 ( 2772) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 336 time to evaluate : 0.729 Fit side-chains REVERT: A 103 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7704 (mt) REVERT: A 413 ASP cc_start: 0.9017 (t70) cc_final: 0.8685 (t0) REVERT: A 468 ARG cc_start: 0.9106 (mmm-85) cc_final: 0.8861 (mmt180) REVERT: A 511 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7752 (ttm-80) REVERT: A 611 ASN cc_start: 0.8526 (p0) cc_final: 0.8181 (p0) REVERT: A 778 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 821 ILE cc_start: 0.9074 (tt) cc_final: 0.8832 (tt) REVERT: A 1044 ILE cc_start: 0.7818 (tt) cc_final: 0.7611 (tt) REVERT: A 1049 ASN cc_start: 0.8424 (t0) cc_final: 0.8093 (t0) REVERT: A 1664 PHE cc_start: 0.8115 (m-80) cc_final: 0.7826 (m-80) REVERT: A 1768 TYR cc_start: 0.8462 (t80) cc_final: 0.7759 (t80) REVERT: A 1899 ASN cc_start: 0.6942 (m-40) cc_final: 0.6032 (p0) REVERT: A 1917 ILE cc_start: 0.8141 (mm) cc_final: 0.7911 (mt) REVERT: A 1985 ASP cc_start: 0.7986 (t0) cc_final: 0.7586 (t0) REVERT: A 2043 ASP cc_start: 0.8307 (t0) cc_final: 0.8084 (t0) outliers start: 16 outliers final: 11 residues processed: 346 average time/residue: 0.1335 time to fit residues: 72.9312 Evaluate side-chains 327 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 315 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 991 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1646 VAL Chi-restraints excluded: chain A residue 1915 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 118 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 136 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 169 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN A1037 ASN A1069 GLN A1338 HIS A1683 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121399 restraints weight = 22227.222| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.83 r_work: 0.3242 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18921 Z= 0.139 Angle : 0.495 7.377 25644 Z= 0.262 Chirality : 0.040 0.169 2965 Planarity : 0.003 0.054 3146 Dihedral : 7.800 73.840 2688 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.55 % Allowed : 9.99 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.18), residues: 2213 helix: 1.68 (0.15), residues: 1254 sheet: -1.59 (0.43), residues: 122 loop : -1.00 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 637 TYR 0.018 0.001 TYR A1574 PHE 0.021 0.001 PHE A2116 TRP 0.019 0.001 TRP A 480 HIS 0.010 0.001 HIS A1499 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (18921) covalent geometry : angle 0.49500 / 0.26 (25644) hydrogen bonds : bond 0.03617 / 2.38 ( 953) hydrogen bonds : angle 4.37726 / 3.16 ( 2772) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 317 time to evaluate : 0.709 Fit side-chains REVERT: A 103 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 413 ASP cc_start: 0.9044 (t70) cc_final: 0.8638 (t0) REVERT: A 468 ARG cc_start: 0.9170 (mmm-85) cc_final: 0.8880 (mmt180) REVERT: A 511 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7840 (ttm-80) REVERT: A 718 ASP cc_start: 0.8593 (t70) cc_final: 0.8313 (t0) REVERT: A 778 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7628 (mt-10) REVERT: A 821 ILE cc_start: 0.9055 (tt) cc_final: 0.8817 (tt) REVERT: A 1049 ASN cc_start: 0.8375 (t0) cc_final: 0.7996 (t0) REVERT: A 1594 GLN cc_start: 0.7590 (pt0) cc_final: 0.7232 (pt0) REVERT: A 1768 TYR cc_start: 0.8492 (t80) cc_final: 0.7890 (t80) REVERT: A 1771 PHE cc_start: 0.7995 (m-80) cc_final: 0.7777 (m-10) REVERT: A 1835 GLU cc_start: 0.7312 (tm-30) cc_final: 0.7082 (tm-30) REVERT: A 1917 ILE cc_start: 0.8163 (mm) cc_final: 0.7904 (mt) REVERT: A 1973 LYS cc_start: 0.7240 (tttt) cc_final: 0.6674 (ttpt) REVERT: A 2043 ASP cc_start: 0.8295 (t0) cc_final: 0.8072 (t0) REVERT: A 2100 ASN cc_start: 0.6847 (m-40) cc_final: 0.6368 (t0) REVERT: B 156 SER cc_start: 0.8959 (p) cc_final: 0.8672 (p) REVERT: E 140 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7419 (mt-10) outliers start: 32 outliers final: 22 residues processed: 335 average time/residue: 0.1347 time to fit residues: 70.9257 Evaluate side-chains 333 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 309 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 991 ASN Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1646 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1915 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 211 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 185 optimal weight: 30.0000 chunk 164 optimal weight: 0.9980 chunk 109 optimal weight: 0.0060 chunk 191 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 991 ASN A1338 HIS A1769 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.158902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120065 restraints weight = 22200.908| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.96 r_work: 0.3254 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18921 Z= 0.104 Angle : 0.464 7.583 25644 Z= 0.245 Chirality : 0.039 0.174 2965 Planarity : 0.003 0.046 3146 Dihedral : 7.618 73.862 2688 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.60 % Allowed : 11.83 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2213 helix: 1.81 (0.15), residues: 1254 sheet: -1.41 (0.44), residues: 120 loop : -0.97 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 137 TYR 0.017 0.001 TYR A1875 PHE 0.018 0.001 PHE A2116 TRP 0.013 0.001 TRP A 480 HIS 0.008 0.001 HIS A1918 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (18921) covalent geometry : angle 0.46389 / 0.25 (25644) hydrogen bonds : bond 0.03348 / 2.21 ( 953) hydrogen bonds : angle 4.22958 / 3.05 ( 2772) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 321 time to evaluate : 0.568 Fit side-chains REVERT: A 103 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7622 (mt) REVERT: A 413 ASP cc_start: 0.9000 (t70) cc_final: 0.8613 (t0) REVERT: A 468 ARG cc_start: 0.9135 (mmm-85) cc_final: 0.8870 (mmt180) REVERT: A 483 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8016 (pp) REVERT: A 511 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7792 (ttm-80) REVERT: A 718 ASP cc_start: 0.8556 (t70) cc_final: 0.8293 (t0) REVERT: A 778 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7678 (mt-10) REVERT: A 821 ILE cc_start: 0.8989 (tt) cc_final: 0.8780 (tt) REVERT: A 1021 ASN cc_start: 0.7738 (t0) cc_final: 0.7270 (t0) REVERT: A 1049 ASN cc_start: 0.8363 (t0) cc_final: 0.7936 (t0) REVERT: A 1594 GLN cc_start: 0.7607 (pt0) cc_final: 0.7206 (pt0) REVERT: A 1768 TYR cc_start: 0.8391 (t80) cc_final: 0.7833 (t80) REVERT: A 1771 PHE cc_start: 0.7997 (m-80) cc_final: 0.7720 (m-10) REVERT: A 1917 ILE cc_start: 0.8121 (mm) cc_final: 0.7851 (mt) REVERT: A 1939 LEU cc_start: 0.3769 (OUTLIER) cc_final: 0.3514 (pp) REVERT: A 1973 LYS cc_start: 0.7259 (tttt) cc_final: 0.6675 (ttpt) REVERT: A 2043 ASP cc_start: 0.8248 (t0) cc_final: 0.8017 (t0) REVERT: B 156 SER cc_start: 0.8901 (p) cc_final: 0.8628 (p) REVERT: E 140 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: E 163 ARG cc_start: 0.8412 (mmm160) cc_final: 0.8084 (mmt180) outliers start: 33 outliers final: 22 residues processed: 339 average time/residue: 0.1180 time to fit residues: 63.3846 Evaluate side-chains 338 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 312 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1572 SER Chi-restraints excluded: chain A residue 1646 VAL Chi-restraints excluded: chain A residue 1939 LEU Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 57 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 175 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 220 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 991 ASN A1022 HIS A1338 HIS ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119151 restraints weight = 22237.838| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.82 r_work: 0.3221 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18921 Z= 0.155 Angle : 0.490 6.919 25644 Z= 0.259 Chirality : 0.040 0.185 2965 Planarity : 0.003 0.040 3146 Dihedral : 7.605 73.914 2688 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.23 % Allowed : 12.61 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2213 helix: 1.79 (0.15), residues: 1256 sheet: -1.50 (0.44), residues: 120 loop : -0.98 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 137 TYR 0.016 0.001 TYR A1574 PHE 0.018 0.001 PHE A 629 TRP 0.017 0.001 TRP A 480 HIS 0.008 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (18921) covalent geometry : angle 0.49024 / 0.26 (25644) hydrogen bonds : bond 0.03566 / 2.36 ( 953) hydrogen bonds : angle 4.23369 / 3.06 ( 2772) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 317 time to evaluate : 0.733 Fit side-chains REVERT: A 102 GLN cc_start: 0.8188 (tp40) cc_final: 0.7931 (tp40) REVERT: A 103 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7781 (mt) REVERT: A 468 ARG cc_start: 0.9189 (mmm-85) cc_final: 0.8931 (mmm160) REVERT: A 483 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8262 (pp) REVERT: A 718 ASP cc_start: 0.8623 (t70) cc_final: 0.8353 (t0) REVERT: A 778 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 875 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7032 (p90) REVERT: A 1021 ASN cc_start: 0.7838 (t0) cc_final: 0.7378 (t0) REVERT: A 1049 ASN cc_start: 0.8411 (t0) cc_final: 0.7997 (t0) REVERT: A 1278 ARG cc_start: 0.8505 (ttm-80) cc_final: 0.8291 (ttm-80) REVERT: A 1594 GLN cc_start: 0.7647 (pt0) cc_final: 0.7247 (pt0) REVERT: A 1835 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 1899 ASN cc_start: 0.6930 (m-40) cc_final: 0.6062 (p0) REVERT: A 1917 ILE cc_start: 0.8232 (mm) cc_final: 0.7959 (mt) REVERT: A 1973 LYS cc_start: 0.7381 (tttt) cc_final: 0.6874 (ttpt) REVERT: A 2100 ASN cc_start: 0.6852 (m-40) cc_final: 0.6372 (t0) REVERT: B 156 SER cc_start: 0.8977 (p) cc_final: 0.8737 (p) REVERT: E 140 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7548 (mt-10) outliers start: 46 outliers final: 32 residues processed: 340 average time/residue: 0.1291 time to fit residues: 69.3760 Evaluate side-chains 346 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 310 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 991 ASN Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1572 SER Chi-restraints excluded: chain A residue 1602 LYS Chi-restraints excluded: chain A residue 1646 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1995 CYS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 127 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 14 optimal weight: 0.0980 chunk 50 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN A1338 HIS ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116261 restraints weight = 22155.718| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.95 r_work: 0.3200 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18921 Z= 0.152 Angle : 0.494 9.676 25644 Z= 0.258 Chirality : 0.040 0.191 2965 Planarity : 0.003 0.043 3146 Dihedral : 7.606 73.961 2688 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.42 % Allowed : 13.00 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2213 helix: 1.78 (0.15), residues: 1263 sheet: -1.49 (0.44), residues: 120 loop : -0.98 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 511 TYR 0.017 0.001 TYR A1574 PHE 0.017 0.001 PHE A 629 TRP 0.012 0.001 TRP A 480 HIS 0.006 0.001 HIS A1918 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (18921) covalent geometry : angle 0.49370 / 0.26 (25644) hydrogen bonds : bond 0.03547 / 2.36 ( 953) hydrogen bonds : angle 4.22677 / 3.05 ( 2772) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 306 time to evaluate : 0.718 Fit side-chains REVERT: A 102 GLN cc_start: 0.8122 (tp40) cc_final: 0.7881 (tp40) REVERT: A 103 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7650 (mt) REVERT: A 468 ARG cc_start: 0.9200 (mmm-85) cc_final: 0.8961 (mmm160) REVERT: A 483 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8190 (pp) REVERT: A 511 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7513 (ttm-80) REVERT: A 718 ASP cc_start: 0.8583 (t70) cc_final: 0.8308 (t0) REVERT: A 875 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.6917 (p90) REVERT: A 1021 ASN cc_start: 0.7713 (t0) cc_final: 0.7275 (t0) REVERT: A 1049 ASN cc_start: 0.8436 (t0) cc_final: 0.7969 (t0) REVERT: A 1594 GLN cc_start: 0.7659 (pt0) cc_final: 0.7210 (pt0) REVERT: A 1899 ASN cc_start: 0.6937 (m-40) cc_final: 0.6028 (p0) REVERT: A 1917 ILE cc_start: 0.8227 (mm) cc_final: 0.7946 (mt) REVERT: A 1973 LYS cc_start: 0.7362 (tttt) cc_final: 0.6859 (ttpt) REVERT: A 2100 ASN cc_start: 0.6777 (m-40) cc_final: 0.6282 (t0) REVERT: B 156 SER cc_start: 0.8942 (p) cc_final: 0.8697 (p) REVERT: C 146 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7347 (mt) REVERT: E 140 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7453 (mt-10) outliers start: 50 outliers final: 35 residues processed: 335 average time/residue: 0.1205 time to fit residues: 64.0098 Evaluate side-chains 342 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 302 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 991 ASN Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1572 SER Chi-restraints excluded: chain A residue 1602 LYS Chi-restraints excluded: chain A residue 1646 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1995 CYS Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 170 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN A 224 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN A1338 HIS A1672 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112310 restraints weight = 22313.718| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.96 r_work: 0.3172 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18921 Z= 0.189 Angle : 0.520 8.278 25644 Z= 0.271 Chirality : 0.042 0.204 2965 Planarity : 0.003 0.048 3146 Dihedral : 7.653 73.990 2688 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.28 % Allowed : 13.58 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2213 helix: 1.71 (0.15), residues: 1269 sheet: -1.43 (0.44), residues: 120 loop : -1.01 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 511 TYR 0.017 0.002 TYR A1126 PHE 0.019 0.002 PHE A 629 TRP 0.011 0.001 TRP A 480 HIS 0.007 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (18921) covalent geometry : angle 0.51992 / 0.27 (25644) hydrogen bonds : bond 0.03740 / 2.49 ( 953) hydrogen bonds : angle 4.28106 / 3.09 ( 2772) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 0.585 Fit side-chains REVERT: A 102 GLN cc_start: 0.8066 (tp40) cc_final: 0.7831 (tp40) REVERT: A 468 ARG cc_start: 0.9236 (mmm-85) cc_final: 0.8976 (mmm160) REVERT: A 483 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8194 (pp) REVERT: A 511 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7555 (ttm-80) REVERT: A 875 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7063 (p90) REVERT: A 1021 ASN cc_start: 0.7728 (t0) cc_final: 0.7242 (t0) REVERT: A 1049 ASN cc_start: 0.8444 (t0) cc_final: 0.7942 (t0) REVERT: A 1631 TYR cc_start: 0.7267 (m-10) cc_final: 0.7044 (m-10) REVERT: A 1771 PHE cc_start: 0.8100 (m-80) cc_final: 0.7892 (m-10) REVERT: A 1835 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7140 (tm-30) REVERT: A 1899 ASN cc_start: 0.6995 (m-40) cc_final: 0.6093 (p0) REVERT: A 1917 ILE cc_start: 0.8189 (mm) cc_final: 0.7912 (mt) REVERT: A 1973 LYS cc_start: 0.7539 (tttt) cc_final: 0.7066 (ttpt) REVERT: A 1986 ASN cc_start: 0.7426 (m110) cc_final: 0.7076 (m-40) REVERT: A 2100 ASN cc_start: 0.6756 (m-40) cc_final: 0.6239 (t0) REVERT: B 156 SER cc_start: 0.8967 (p) cc_final: 0.8739 (p) REVERT: C 146 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7321 (mt) REVERT: E 140 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7430 (mt-10) outliers start: 47 outliers final: 35 residues processed: 327 average time/residue: 0.1212 time to fit residues: 63.4124 Evaluate side-chains 333 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 294 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 991 ASN Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1572 SER Chi-restraints excluded: chain A residue 1646 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1995 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 190 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 212 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN A 220 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1338 HIS A1594 GLN A1599 HIS A1672 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1975 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110399 restraints weight = 22144.803| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.94 r_work: 0.3146 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 18921 Z= 0.229 Angle : 0.556 9.021 25644 Z= 0.290 Chirality : 0.043 0.218 2965 Planarity : 0.004 0.043 3146 Dihedral : 7.760 74.012 2688 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.33 % Allowed : 14.26 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 2213 helix: 1.60 (0.15), residues: 1264 sheet: -1.46 (0.45), residues: 120 loop : -1.06 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 511 TYR 0.018 0.002 TYR A1126 PHE 0.022 0.002 PHE A 629 TRP 0.012 0.001 TRP A 480 HIS 0.011 0.001 HIS A1918 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 (18921) covalent geometry : angle 0.55599 / 0.29 (25644) hydrogen bonds : bond 0.03983 / 2.65 ( 953) hydrogen bonds : angle 4.36625 / 3.15 ( 2772) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 0.629 Fit side-chains REVERT: A 102 GLN cc_start: 0.8091 (tp40) cc_final: 0.7828 (tp40) REVERT: A 103 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7639 (mt) REVERT: A 483 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8237 (pp) REVERT: A 511 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7480 (ttm-80) REVERT: A 875 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7259 (p90) REVERT: A 1021 ASN cc_start: 0.7755 (t0) cc_final: 0.7227 (t0) REVERT: A 1049 ASN cc_start: 0.8380 (t0) cc_final: 0.7863 (t0) REVERT: A 1594 GLN cc_start: 0.7656 (pt0) cc_final: 0.7173 (pt0) REVERT: A 1631 TYR cc_start: 0.7335 (m-10) cc_final: 0.7134 (m-10) REVERT: A 1771 PHE cc_start: 0.8128 (m-80) cc_final: 0.7922 (m-10) REVERT: A 1835 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7095 (tm-30) REVERT: A 1899 ASN cc_start: 0.7020 (m-40) cc_final: 0.6141 (p0) REVERT: A 1973 LYS cc_start: 0.7616 (tttt) cc_final: 0.7178 (ttpt) REVERT: A 1986 ASN cc_start: 0.7580 (m110) cc_final: 0.7224 (m-40) REVERT: A 2100 ASN cc_start: 0.6780 (m-40) cc_final: 0.6236 (t0) REVERT: B 156 SER cc_start: 0.9011 (p) cc_final: 0.8793 (p) REVERT: C 146 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7383 (mt) REVERT: E 140 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7321 (mt-10) outliers start: 48 outliers final: 38 residues processed: 312 average time/residue: 0.1298 time to fit residues: 64.2287 Evaluate side-chains 323 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1572 SER Chi-restraints excluded: chain A residue 1646 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1672 ASN Chi-restraints excluded: chain A residue 1908 ILE Chi-restraints excluded: chain A residue 1995 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 190 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 991 ASN A1338 HIS A1599 HIS A1672 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116371 restraints weight = 22036.930| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.77 r_work: 0.3204 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18921 Z= 0.127 Angle : 0.500 8.193 25644 Z= 0.264 Chirality : 0.040 0.246 2965 Planarity : 0.003 0.040 3146 Dihedral : 7.685 74.013 2688 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.04 % Allowed : 14.84 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.18), residues: 2213 helix: 1.77 (0.15), residues: 1252 sheet: -1.44 (0.44), residues: 120 loop : -0.98 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 511 TYR 0.018 0.001 TYR A1574 PHE 0.016 0.001 PHE A1534 TRP 0.010 0.001 TRP A 732 HIS 0.012 0.001 HIS A1918 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (18921) covalent geometry : angle 0.50009 / 0.26 (25644) hydrogen bonds : bond 0.03607 / 2.40 ( 953) hydrogen bonds : angle 4.26501 / 3.07 ( 2772) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 0.698 Fit side-chains REVERT: A 102 GLN cc_start: 0.8102 (tp40) cc_final: 0.7828 (tp40) REVERT: A 103 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7764 (mt) REVERT: A 483 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8236 (pp) REVERT: A 511 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7709 (ttm-80) REVERT: A 875 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7006 (p90) REVERT: A 1021 ASN cc_start: 0.7859 (t0) cc_final: 0.7392 (t0) REVERT: A 1049 ASN cc_start: 0.8380 (t0) cc_final: 0.8152 (t0) REVERT: A 1835 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 1899 ASN cc_start: 0.6956 (m-40) cc_final: 0.6235 (p0) REVERT: A 1973 LYS cc_start: 0.7625 (tttt) cc_final: 0.7198 (ttpt) REVERT: A 1985 ASP cc_start: 0.8185 (t0) cc_final: 0.7865 (t0) REVERT: A 1986 ASN cc_start: 0.7505 (m110) cc_final: 0.7160 (m-40) REVERT: A 2100 ASN cc_start: 0.6881 (m-40) cc_final: 0.6327 (t0) REVERT: B 156 SER cc_start: 0.9024 (p) cc_final: 0.8812 (p) REVERT: C 146 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7598 (mt) REVERT: E 140 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7551 (mt-10) outliers start: 42 outliers final: 34 residues processed: 312 average time/residue: 0.1156 time to fit residues: 57.0884 Evaluate side-chains 322 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 283 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 991 ASN Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1572 SER Chi-restraints excluded: chain A residue 1646 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1672 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1995 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 73 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 105 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 991 ASN A1338 HIS A1599 HIS A1672 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.154886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115977 restraints weight = 22080.025| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.93 r_work: 0.3191 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18921 Z= 0.112 Angle : 0.490 7.746 25644 Z= 0.259 Chirality : 0.040 0.255 2965 Planarity : 0.003 0.040 3146 Dihedral : 7.617 74.012 2688 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.84 % Rotamer: Outliers : 1.79 % Allowed : 15.42 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2213 helix: 1.81 (0.15), residues: 1259 sheet: -1.42 (0.44), residues: 120 loop : -0.94 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1000 TYR 0.018 0.001 TYR A1574 PHE 0.024 0.001 PHE A1771 TRP 0.011 0.001 TRP A 732 HIS 0.012 0.001 HIS A1918 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (18921) covalent geometry : angle 0.48972 / 0.26 (25644) hydrogen bonds : bond 0.03455 / 2.30 ( 953) hydrogen bonds : angle 4.20164 / 3.02 ( 2772) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 0.649 Fit side-chains REVERT: A 102 GLN cc_start: 0.8072 (tp40) cc_final: 0.7787 (tp40) REVERT: A 103 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7617 (mt) REVERT: A 483 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8122 (pp) REVERT: A 511 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7572 (ttm-80) REVERT: A 687 ASN cc_start: 0.8562 (m110) cc_final: 0.8325 (m-40) REVERT: A 875 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.6972 (p90) REVERT: A 991 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7941 (p0) REVERT: A 1021 ASN cc_start: 0.7759 (t0) cc_final: 0.7267 (t0) REVERT: A 1049 ASN cc_start: 0.8316 (t0) cc_final: 0.8061 (t0) REVERT: A 1835 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 1899 ASN cc_start: 0.6913 (m-40) cc_final: 0.6193 (p0) REVERT: A 1951 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7614 (mm-30) REVERT: A 1973 LYS cc_start: 0.7468 (tttt) cc_final: 0.7014 (ttpt) REVERT: A 1985 ASP cc_start: 0.8194 (t0) cc_final: 0.7879 (t0) REVERT: A 1986 ASN cc_start: 0.7507 (m110) cc_final: 0.7158 (m-40) REVERT: A 2100 ASN cc_start: 0.6767 (m-40) cc_final: 0.6235 (t0) REVERT: B 156 SER cc_start: 0.8948 (p) cc_final: 0.8734 (p) REVERT: C 146 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7321 (mt) REVERT: E 140 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7436 (mt-10) outliers start: 37 outliers final: 29 residues processed: 318 average time/residue: 0.1284 time to fit residues: 64.1242 Evaluate side-chains 323 residues out of total 2062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 288 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 991 ASN Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1428 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1572 SER Chi-restraints excluded: chain A residue 1646 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1672 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1995 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 118 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 139 optimal weight: 0.0870 chunk 220 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A1338 HIS A1417 ASN A1599 HIS A1672 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116968 restraints weight = 22183.267| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.78 r_work: 0.3206 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18921 Z= 0.137 Angle : 0.511 11.488 25644 Z= 0.266 Chirality : 0.040 0.256 2965 Planarity : 0.003 0.040 3146 Dihedral : 7.612 74.003 2688 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 1.89 % Allowed : 15.66 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.18), residues: 2213 helix: 1.82 (0.15), residues: 1253 sheet: -1.39 (0.44), residues: 120 loop : -0.92 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 511 TYR 0.033 0.001 TYR A1574 PHE 0.027 0.002 PHE A1771 TRP 0.010 0.001 TRP A 732 HIS 0.011 0.001 HIS A1918 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (18921) covalent geometry : angle 0.51060 / 0.27 (25644) hydrogen bonds : bond 0.03512 / 2.34 ( 953) hydrogen bonds : angle 4.20715 / 3.03 ( 2772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4340.13 seconds wall clock time: 75 minutes 23.61 seconds (4523.61 seconds total)