Starting phenix.real_space_refine on Sat Jun 28 03:29:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iz0_61006/06_2025/9iz0_61006.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iz0_61006/06_2025/9iz0_61006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iz0_61006/06_2025/9iz0_61006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iz0_61006/06_2025/9iz0_61006.map" model { file = "/net/cci-nas-00/data/ceres_data/9iz0_61006/06_2025/9iz0_61006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iz0_61006/06_2025/9iz0_61006.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 20181 2.51 5 N 5707 2.21 5 O 6114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32048 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "A" Number of atoms: 15929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2430, 15929 Classifications: {'peptide': 2430} Incomplete info: {'truncation_to_alanine': 1157} Link IDs: {'PTRANS': 70, 'TRANS': 2359} Chain breaks: 28 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 4263 Unresolved non-hydrogen angles: 5439 Unresolved non-hydrogen dihedrals: 3647 Unresolved non-hydrogen chiralities: 368 Planarities with less than four sites: {'GLN:plan1': 46, 'HIS:plan': 25, 'TYR:plan': 56, 'ASN:plan1': 59, 'TRP:plan': 17, 'ASP:plan': 59, 'PHE:plan': 98, 'GLU:plan': 68, 'ARG:plan': 50} Unresolved non-hydrogen planarities: 2318 Chain: "B" Number of atoms: 15993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2424, 15993 Classifications: {'peptide': 2424} Incomplete info: {'truncation_to_alanine': 1134} Link IDs: {'PTRANS': 71, 'TRANS': 2352} Chain breaks: 46 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 4173 Unresolved non-hydrogen angles: 5322 Unresolved non-hydrogen dihedrals: 3583 Unresolved non-hydrogen chiralities: 353 Planarities with less than four sites: {'GLN:plan1': 44, 'HIS:plan': 30, 'TYR:plan': 58, 'ASN:plan1': 53, 'TRP:plan': 16, 'ASP:plan': 58, 'PHE:plan': 93, 'GLU:plan': 66, 'ARG:plan': 48} Unresolved non-hydrogen planarities: 2271 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.75, per 1000 atoms: 0.62 Number of scatterers: 32048 At special positions: 0 Unit cell: (100.58, 182.97, 222.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 6 15.00 O 6114 8.00 N 5707 7.00 C 20181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A2166 " - pdb=" SG CYS A2257 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.48 Conformation dependent library (CDL) restraints added in 4.9 seconds 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9482 Finding SS restraints... Secondary structure from input PDB file: 270 helices and 5 sheets defined 69.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.17 Creating SS restraints... Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 122 through 135 removed outlier: 3.951A pdb=" N LEU A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 164 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 220 through 238 removed outlier: 4.043A pdb=" N PHE A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 261 removed outlier: 3.947A pdb=" N ALA A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 285 removed outlier: 3.581A pdb=" N TRP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 314 through 333 removed outlier: 3.705A pdb=" N ARG A 318 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 396 removed outlier: 4.292A pdb=" N TYR A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 430 through 449 removed outlier: 4.036A pdb=" N VAL A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 Processing helix chain 'A' and resid 470 through 486 Processing helix chain 'A' and resid 492 through 510 Processing helix chain 'A' and resid 518 through 522 Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.691A pdb=" N PHE A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 566 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 646 through 651 removed outlier: 4.339A pdb=" N ALA A 650 " --> pdb=" O HIS A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 697 removed outlier: 3.581A pdb=" N CYS A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 715 Processing helix chain 'A' and resid 759 through 770 removed outlier: 3.655A pdb=" N SER A 770 " --> pdb=" O LYS A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 789 Processing helix chain 'A' and resid 790 through 793 Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 816 through 828 removed outlier: 4.368A pdb=" N ASP A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET A 823 " --> pdb=" O TYR A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 4.053A pdb=" N GLN A 870 " --> pdb=" O GLY A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 901 Processing helix chain 'A' and resid 902 through 909 removed outlier: 3.913A pdb=" N PHE A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 919 Processing helix chain 'A' and resid 924 through 942 removed outlier: 3.719A pdb=" N PHE A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 948 removed outlier: 3.773A pdb=" N GLU A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 948 " --> pdb=" O ASP A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 966 Processing helix chain 'A' and resid 973 through 985 Processing helix chain 'A' and resid 986 through 992 Processing helix chain 'A' and resid 997 through 1009 Processing helix chain 'A' and resid 1020 through 1031 Processing helix chain 'A' and resid 1033 through 1048 Processing helix chain 'A' and resid 1053 through 1064 removed outlier: 3.872A pdb=" N PHE A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) Proline residue: A1062 - end of helix Processing helix chain 'A' and resid 1067 through 1073 Processing helix chain 'A' and resid 1074 through 1089 Processing helix chain 'A' and resid 1092 through 1104 Processing helix chain 'A' and resid 1108 through 1113 Processing helix chain 'A' and resid 1129 through 1137 Processing helix chain 'A' and resid 1168 through 1183 removed outlier: 3.935A pdb=" N GLU A1176 " --> pdb=" O GLU A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1197 Processing helix chain 'A' and resid 1200 through 1220 removed outlier: 4.476A pdb=" N GLN A1207 " --> pdb=" O GLU A1203 " (cutoff:3.500A) Proline residue: A1210 - end of helix Processing helix chain 'A' and resid 1240 through 1255 Processing helix chain 'A' and resid 1270 through 1280 Processing helix chain 'A' and resid 1300 through 1311 removed outlier: 3.795A pdb=" N TRP A1304 " --> pdb=" O LYS A1300 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE A1310 " --> pdb=" O CYS A1306 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A1311 " --> pdb=" O ASN A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1334 removed outlier: 3.569A pdb=" N ILE A1323 " --> pdb=" O ILE A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1357 Processing helix chain 'A' and resid 1358 through 1362 Processing helix chain 'A' and resid 1363 through 1380 Processing helix chain 'A' and resid 1380 through 1402 removed outlier: 4.300A pdb=" N SER A1385 " --> pdb=" O PRO A1381 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A1386 " --> pdb=" O CYS A1382 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A1392 " --> pdb=" O LEU A1388 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE A1393 " --> pdb=" O GLY A1389 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N HIS A1394 " --> pdb=" O ILE A1390 " (cutoff:3.500A) Proline residue: A1400 - end of helix Processing helix chain 'A' and resid 1407 through 1414 removed outlier: 3.988A pdb=" N MET A1414 " --> pdb=" O ALA A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1449 removed outlier: 4.594A pdb=" N PHE A1448 " --> pdb=" O ALA A1444 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A1449 " --> pdb=" O LEU A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1465 removed outlier: 3.938A pdb=" N GLN A1459 " --> pdb=" O PHE A1455 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A1463 " --> pdb=" O GLN A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1479 removed outlier: 4.159A pdb=" N SER A1477 " --> pdb=" O TRP A1473 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A1479 " --> pdb=" O GLU A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1499 removed outlier: 4.332A pdb=" N CYS A1497 " --> pdb=" O ASN A1493 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A1498 " --> pdb=" O ASN A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1501 through 1507 Processing helix chain 'A' and resid 1508 through 1515 Processing helix chain 'A' and resid 1517 through 1522 Processing helix chain 'A' and resid 1532 through 1549 Processing helix chain 'A' and resid 1571 through 1594 removed outlier: 3.933A pdb=" N LYS A1594 " --> pdb=" O SER A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1610 Processing helix chain 'A' and resid 1627 through 1634 removed outlier: 4.005A pdb=" N ILE A1631 " --> pdb=" O LYS A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1671 Processing helix chain 'A' and resid 1678 through 1690 removed outlier: 3.947A pdb=" N SER A1682 " --> pdb=" O SER A1678 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET A1690 " --> pdb=" O LEU A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1710 removed outlier: 3.918A pdb=" N SER A1694 " --> pdb=" O MET A1690 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR A1695 " --> pdb=" O VAL A1691 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A1698 " --> pdb=" O SER A1694 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN A1699 " --> pdb=" O THR A1695 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR A1700 " --> pdb=" O SER A1696 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A1701 " --> pdb=" O ILE A1697 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N HIS A1703 " --> pdb=" O GLN A1699 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU A1704 " --> pdb=" O TYR A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1717 through 1731 removed outlier: 4.674A pdb=" N THR A1723 " --> pdb=" O LYS A1719 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1736 through 1752 removed outlier: 3.506A pdb=" N GLN A1752 " --> pdb=" O TYR A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1765 Processing helix chain 'A' and resid 1770 through 1781 removed outlier: 3.591A pdb=" N ALA A1774 " --> pdb=" O ASN A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1798 removed outlier: 3.538A pdb=" N SER A1787 " --> pdb=" O LEU A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1813 Processing helix chain 'A' and resid 1827 through 1839 Processing helix chain 'A' and resid 1844 through 1856 removed outlier: 3.755A pdb=" N LEU A1848 " --> pdb=" O ALA A1844 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1874 Processing helix chain 'A' and resid 1875 through 1889 Processing helix chain 'A' and resid 1896 through 1907 removed outlier: 3.930A pdb=" N TYR A1900 " --> pdb=" O SER A1896 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A1905 " --> pdb=" O ALA A1901 " (cutoff:3.500A) Processing helix chain 'A' and resid 1921 through 1939 removed outlier: 3.956A pdb=" N TYR A1939 " --> pdb=" O ASN A1935 " (cutoff:3.500A) Processing helix chain 'A' and resid 1943 through 1955 removed outlier: 4.187A pdb=" N LEU A1955 " --> pdb=" O LYS A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1963 through 1978 Processing helix chain 'A' and resid 1989 through 1995 Processing helix chain 'A' and resid 2003 through 2007 Processing helix chain 'A' and resid 2009 through 2022 removed outlier: 3.697A pdb=" N ILE A2013 " --> pdb=" O LEU A2009 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A2022 " --> pdb=" O LEU A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2024 through 2029 Processing helix chain 'A' and resid 2031 through 2037 Processing helix chain 'A' and resid 2039 through 2049 removed outlier: 4.461A pdb=" N GLU A2043 " --> pdb=" O TYR A2039 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A2049 " --> pdb=" O LEU A2045 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2075 removed outlier: 3.820A pdb=" N ASP A2075 " --> pdb=" O TYR A2071 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2096 Processing helix chain 'A' and resid 2098 through 2111 removed outlier: 3.957A pdb=" N SER A2109 " --> pdb=" O MET A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2119 through 2133 removed outlier: 3.530A pdb=" N TYR A2123 " --> pdb=" O PRO A2119 " (cutoff:3.500A) Processing helix chain 'A' and resid 2137 through 2145 Processing helix chain 'A' and resid 2146 through 2152 Processing helix chain 'A' and resid 2158 through 2177 removed outlier: 3.734A pdb=" N ALA A2162 " --> pdb=" O ALA A2158 " (cutoff:3.500A) Processing helix chain 'A' and resid 2178 through 2204 Processing helix chain 'A' and resid 2219 through 2261 removed outlier: 3.910A pdb=" N SER A2261 " --> pdb=" O CYS A2257 " (cutoff:3.500A) Processing helix chain 'A' and resid 2266 through 2276 removed outlier: 3.528A pdb=" N ARG A2270 " --> pdb=" O VAL A2266 " (cutoff:3.500A) Processing helix chain 'A' and resid 2281 through 2293 removed outlier: 3.789A pdb=" N ASN A2285 " --> pdb=" O LEU A2281 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A2287 " --> pdb=" O GLU A2283 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A2288 " --> pdb=" O LEU A2284 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR A2291 " --> pdb=" O SER A2287 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A2293 " --> pdb=" O GLN A2289 " (cutoff:3.500A) Processing helix chain 'A' and resid 2294 through 2295 No H-bonds generated for 'chain 'A' and resid 2294 through 2295' Processing helix chain 'A' and resid 2296 through 2301 removed outlier: 3.617A pdb=" N ILE A2301 " --> pdb=" O LYS A2298 " (cutoff:3.500A) Processing helix chain 'A' and resid 2303 through 2311 removed outlier: 3.545A pdb=" N LEU A2311 " --> pdb=" O LEU A2307 " (cutoff:3.500A) Processing helix chain 'A' and resid 2316 through 2333 Processing helix chain 'A' and resid 2333 through 2346 removed outlier: 3.638A pdb=" N SER A2337 " --> pdb=" O HIS A2333 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N HIS A2339 " --> pdb=" O TYR A2335 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL A2340 " --> pdb=" O HIS A2336 " (cutoff:3.500A) Processing helix chain 'A' and resid 2354 through 2373 removed outlier: 3.675A pdb=" N SER A2358 " --> pdb=" O LEU A2354 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A2373 " --> pdb=" O LEU A2369 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2396 removed outlier: 3.853A pdb=" N TRP A2396 " --> pdb=" O SER A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2418 removed outlier: 3.569A pdb=" N LEU A2417 " --> pdb=" O TYR A2413 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A2418 " --> pdb=" O LYS A2414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2413 through 2418' Processing helix chain 'A' and resid 2418 through 2423 Processing helix chain 'A' and resid 2485 through 2505 Processing helix chain 'A' and resid 2507 through 2512 removed outlier: 3.730A pdb=" N ARG A2512 " --> pdb=" O LYS A2508 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2552 Processing helix chain 'A' and resid 2557 through 2569 removed outlier: 3.509A pdb=" N CYS A2561 " --> pdb=" O SER A2557 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A2563 " --> pdb=" O SER A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2572 through 2587 Processing helix chain 'A' and resid 2590 through 2594 Processing helix chain 'A' and resid 2601 through 2626 Processing helix chain 'A' and resid 2632 through 2634 No H-bonds generated for 'chain 'A' and resid 2632 through 2634' Processing helix chain 'A' and resid 2671 through 2678 removed outlier: 3.602A pdb=" N VAL A2675 " --> pdb=" O THR A2671 " (cutoff:3.500A) Processing helix chain 'A' and resid 2685 through 2701 Processing helix chain 'A' and resid 2701 through 2715 removed outlier: 3.596A pdb=" N ASP A2715 " --> pdb=" O VAL A2711 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2778 removed outlier: 4.266A pdb=" N ARG A2769 " --> pdb=" O SER A2765 " (cutoff:3.500A) Processing helix chain 'A' and resid 2783 through 2797 Processing helix chain 'A' and resid 2797 through 2804 removed outlier: 4.301A pdb=" N LEU A2803 " --> pdb=" O SER A2799 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET A2804 " --> pdb=" O TYR A2800 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.773A pdb=" N THR B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 220 through 236 removed outlier: 3.819A pdb=" N VAL B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 261 Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.785A pdb=" N TRP B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 314 through 334 Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 390 through 397 removed outlier: 3.523A pdb=" N LYS B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 430 through 449 removed outlier: 6.424A pdb=" N ALA B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE B 447 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 468 Processing helix chain 'B' and resid 470 through 486 removed outlier: 3.732A pdb=" N TYR B 486 " --> pdb=" O PHE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 507 through 512 removed outlier: 3.976A pdb=" N LEU B 511 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 515 No H-bonds generated for 'chain 'B' and resid 514 through 515' Processing helix chain 'B' and resid 517 through 517 No H-bonds generated for 'chain 'B' and resid 517 through 517' Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 609 through 622 removed outlier: 4.177A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 651 Processing helix chain 'B' and resid 653 through 655 No H-bonds generated for 'chain 'B' and resid 653 through 655' Processing helix chain 'B' and resid 680 through 697 Processing helix chain 'B' and resid 702 through 715 removed outlier: 3.837A pdb=" N TYR B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 771 removed outlier: 3.886A pdb=" N HIS B 769 " --> pdb=" O VAL B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.961A pdb=" N CYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 811 removed outlier: 3.590A pdb=" N ASP B 809 " --> pdb=" O THR B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 828 Processing helix chain 'B' and resid 866 through 885 removed outlier: 4.166A pdb=" N GLN B 870 " --> pdb=" O GLY B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 901 removed outlier: 3.529A pdb=" N TYR B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 909 Processing helix chain 'B' and resid 909 through 919 removed outlier: 3.569A pdb=" N ILE B 913 " --> pdb=" O GLY B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 942 removed outlier: 3.643A pdb=" N ASN B 942 " --> pdb=" O LYS B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 948 removed outlier: 3.660A pdb=" N GLU B 946 " --> pdb=" O ASN B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 963 Processing helix chain 'B' and resid 972 through 986 removed outlier: 3.838A pdb=" N LYS B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 991 removed outlier: 3.754A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1009 Processing helix chain 'B' and resid 1020 through 1031 Processing helix chain 'B' and resid 1034 through 1047 Processing helix chain 'B' and resid 1052 through 1064 Proline residue: B1062 - end of helix Processing helix chain 'B' and resid 1067 through 1073 Processing helix chain 'B' and resid 1074 through 1089 Processing helix chain 'B' and resid 1092 through 1104 Processing helix chain 'B' and resid 1114 through 1118 Processing helix chain 'B' and resid 1129 through 1137 Processing helix chain 'B' and resid 1168 through 1183 removed outlier: 4.497A pdb=" N LEU B1179 " --> pdb=" O ASP B1175 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B1180 " --> pdb=" O GLU B1176 " (cutoff:3.500A) Processing helix chain 'B' and resid 1187 through 1197 Processing helix chain 'B' and resid 1200 through 1220 removed outlier: 3.935A pdb=" N GLN B1207 " --> pdb=" O GLU B1203 " (cutoff:3.500A) Proline residue: B1210 - end of helix Processing helix chain 'B' and resid 1240 through 1255 Processing helix chain 'B' and resid 1270 through 1280 Processing helix chain 'B' and resid 1300 through 1312 Processing helix chain 'B' and resid 1319 through 1334 removed outlier: 4.285A pdb=" N ILE B1323 " --> pdb=" O ILE B1319 " (cutoff:3.500A) Processing helix chain 'B' and resid 1339 through 1357 Processing helix chain 'B' and resid 1358 through 1362 Processing helix chain 'B' and resid 1363 through 1380 removed outlier: 3.594A pdb=" N ILE B1380 " --> pdb=" O GLN B1376 " (cutoff:3.500A) Processing helix chain 'B' and resid 1383 through 1403 Proline residue: B1400 - end of helix removed outlier: 4.231A pdb=" N PHE B1403 " --> pdb=" O LYS B1399 " (cutoff:3.500A) Processing helix chain 'B' and resid 1407 through 1414 removed outlier: 3.728A pdb=" N MET B1414 " --> pdb=" O ALA B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1428 through 1439 Processing helix chain 'B' and resid 1442 through 1449 removed outlier: 4.171A pdb=" N PHE B1448 " --> pdb=" O ALA B1444 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B1449 " --> pdb=" O LEU B1445 " (cutoff:3.500A) Processing helix chain 'B' and resid 1455 through 1464 Processing helix chain 'B' and resid 1469 through 1480 Processing helix chain 'B' and resid 1502 through 1507 removed outlier: 3.629A pdb=" N ALA B1506 " --> pdb=" O GLN B1502 " (cutoff:3.500A) Processing helix chain 'B' and resid 1508 through 1515 Processing helix chain 'B' and resid 1516 through 1520 Processing helix chain 'B' and resid 1532 through 1549 removed outlier: 3.723A pdb=" N LYS B1549 " --> pdb=" O TRP B1545 " (cutoff:3.500A) Processing helix chain 'B' and resid 1574 through 1595 Processing helix chain 'B' and resid 1598 through 1609 Processing helix chain 'B' and resid 1627 through 1634 removed outlier: 3.611A pdb=" N ILE B1631 " --> pdb=" O LYS B1627 " (cutoff:3.500A) Processing helix chain 'B' and resid 1660 through 1672 removed outlier: 4.082A pdb=" N LYS B1664 " --> pdb=" O SER B1660 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B1672 " --> pdb=" O LEU B1668 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1686 Processing helix chain 'B' and resid 1690 through 1691 No H-bonds generated for 'chain 'B' and resid 1690 through 1691' Processing helix chain 'B' and resid 1693 through 1694 No H-bonds generated for 'chain 'B' and resid 1693 through 1694' Processing helix chain 'B' and resid 1695 through 1710 removed outlier: 4.701A pdb=" N HIS B1703 " --> pdb=" O GLN B1699 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B1704 " --> pdb=" O TYR B1700 " (cutoff:3.500A) Processing helix chain 'B' and resid 1716 through 1731 removed outlier: 4.116A pdb=" N GLU B1720 " --> pdb=" O LYS B1716 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B1731 " --> pdb=" O LEU B1727 " (cutoff:3.500A) Processing helix chain 'B' and resid 1735 through 1752 removed outlier: 4.353A pdb=" N ARG B1739 " --> pdb=" O THR B1735 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B1752 " --> pdb=" O TYR B1748 " (cutoff:3.500A) Processing helix chain 'B' and resid 1759 through 1765 Processing helix chain 'B' and resid 1770 through 1781 removed outlier: 3.680A pdb=" N ALA B1774 " --> pdb=" O ASN B1770 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1798 Processing helix chain 'B' and resid 1802 through 1812 removed outlier: 3.883A pdb=" N GLN B1812 " --> pdb=" O ASP B1808 " (cutoff:3.500A) Processing helix chain 'B' and resid 1829 through 1839 removed outlier: 3.631A pdb=" N GLU B1838 " --> pdb=" O LYS B1834 " (cutoff:3.500A) Processing helix chain 'B' and resid 1844 through 1856 removed outlier: 3.702A pdb=" N TYR B1854 " --> pdb=" O ALA B1850 " (cutoff:3.500A) Processing helix chain 'B' and resid 1862 through 1874 removed outlier: 4.514A pdb=" N SER B1867 " --> pdb=" O LYS B1863 " (cutoff:3.500A) Processing helix chain 'B' and resid 1875 through 1890 Processing helix chain 'B' and resid 1900 through 1906 removed outlier: 4.091A pdb=" N TRP B1904 " --> pdb=" O TYR B1900 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG B1905 " --> pdb=" O ALA B1901 " (cutoff:3.500A) Processing helix chain 'B' and resid 1921 through 1940 Processing helix chain 'B' and resid 1941 through 1955 removed outlier: 3.738A pdb=" N LEU B1955 " --> pdb=" O LYS B1951 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1960 removed outlier: 3.631A pdb=" N ASN B1959 " --> pdb=" O ILE B1956 " (cutoff:3.500A) Processing helix chain 'B' and resid 1963 through 1980 removed outlier: 3.719A pdb=" N CYS B1980 " --> pdb=" O PHE B1976 " (cutoff:3.500A) Processing helix chain 'B' and resid 1990 through 1997 Processing helix chain 'B' and resid 2002 through 2007 removed outlier: 3.559A pdb=" N CYS B2006 " --> pdb=" O GLN B2002 " (cutoff:3.500A) Processing helix chain 'B' and resid 2012 through 2013 No H-bonds generated for 'chain 'B' and resid 2012 through 2013' Processing helix chain 'B' and resid 2015 through 2017 No H-bonds generated for 'chain 'B' and resid 2015 through 2017' Processing helix chain 'B' and resid 2018 through 2018 No H-bonds generated for 'chain 'B' and resid 2018 through 2018' Processing helix chain 'B' and resid 2021 through 2024 No H-bonds generated for 'chain 'B' and resid 2021 through 2024' Processing helix chain 'B' and resid 2024 through 2029 Processing helix chain 'B' and resid 2030 through 2038 removed outlier: 4.239A pdb=" N ALA B2034 " --> pdb=" O SER B2030 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B2038 " --> pdb=" O ALA B2034 " (cutoff:3.500A) Processing helix chain 'B' and resid 2040 through 2040 No H-bonds generated for 'chain 'B' and resid 2040 through 2040' Processing helix chain 'B' and resid 2043 through 2049 Processing helix chain 'B' and resid 2056 through 2074 removed outlier: 3.672A pdb=" N LEU B2066 " --> pdb=" O SER B2062 " (cutoff:3.500A) Processing helix chain 'B' and resid 2080 through 2096 Processing helix chain 'B' and resid 2098 through 2111 Processing helix chain 'B' and resid 2121 through 2133 Processing helix chain 'B' and resid 2140 through 2141 No H-bonds generated for 'chain 'B' and resid 2140 through 2141' Processing helix chain 'B' and resid 2143 through 2144 No H-bonds generated for 'chain 'B' and resid 2143 through 2144' Processing helix chain 'B' and resid 2145 through 2153 removed outlier: 3.515A pdb=" N SER B2149 " --> pdb=" O TYR B2145 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2165 removed outlier: 3.834A pdb=" N ALA B2162 " --> pdb=" O ALA B2158 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS B2163 " --> pdb=" O LYS B2159 " (cutoff:3.500A) Processing helix chain 'B' and resid 2168 through 2178 Processing helix chain 'B' and resid 2178 through 2194 Processing helix chain 'B' and resid 2197 through 2204 Processing helix chain 'B' and resid 2219 through 2261 removed outlier: 3.583A pdb=" N SER B2261 " --> pdb=" O CYS B2257 " (cutoff:3.500A) Processing helix chain 'B' and resid 2266 through 2278 removed outlier: 3.957A pdb=" N ARG B2270 " --> pdb=" O VAL B2266 " (cutoff:3.500A) Processing helix chain 'B' and resid 2282 through 2293 removed outlier: 4.487A pdb=" N HIS B2290 " --> pdb=" O ASN B2286 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B2293 " --> pdb=" O GLN B2289 " (cutoff:3.500A) Processing helix chain 'B' and resid 2300 through 2310 removed outlier: 4.252A pdb=" N TYR B2305 " --> pdb=" O ILE B2301 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLN B2306 " --> pdb=" O PRO B2302 " (cutoff:3.500A) Processing helix chain 'B' and resid 2318 through 2333 removed outlier: 3.666A pdb=" N LEU B2322 " --> pdb=" O PHE B2318 " (cutoff:3.500A) Processing helix chain 'B' and resid 2337 through 2346 removed outlier: 3.545A pdb=" N LEU B2344 " --> pdb=" O VAL B2340 " (cutoff:3.500A) Processing helix chain 'B' and resid 2354 through 2373 removed outlier: 3.641A pdb=" N SER B2358 " --> pdb=" O LEU B2354 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG B2361 " --> pdb=" O GLY B2357 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN B2373 " --> pdb=" O LEU B2369 " (cutoff:3.500A) Processing helix chain 'B' and resid 2373 through 2396 removed outlier: 4.105A pdb=" N ASN B2378 " --> pdb=" O GLN B2374 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU B2379 " --> pdb=" O GLY B2375 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2423 removed outlier: 4.599A pdb=" N ALA B2420 " --> pdb=" O PHE B2416 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA B2421 " --> pdb=" O LEU B2417 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B2423 " --> pdb=" O ASP B2419 " (cutoff:3.500A) Processing helix chain 'B' and resid 2485 through 2505 removed outlier: 3.749A pdb=" N ASP B2489 " --> pdb=" O ASP B2485 " (cutoff:3.500A) Processing helix chain 'B' and resid 2506 through 2512 Processing helix chain 'B' and resid 2547 through 2552 removed outlier: 3.672A pdb=" N HIS B2552 " --> pdb=" O HIS B2548 " (cutoff:3.500A) Processing helix chain 'B' and resid 2557 through 2568 removed outlier: 3.564A pdb=" N CYS B2561 " --> pdb=" O SER B2557 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG B2562 " --> pdb=" O LEU B2558 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS B2563 " --> pdb=" O SER B2559 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B2564 " --> pdb=" O THR B2560 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B2568 " --> pdb=" O LEU B2564 " (cutoff:3.500A) Processing helix chain 'B' and resid 2572 through 2587 removed outlier: 3.641A pdb=" N ARG B2576 " --> pdb=" O ASP B2572 " (cutoff:3.500A) Processing helix chain 'B' and resid 2591 through 2596 removed outlier: 4.243A pdb=" N PHE B2595 " --> pdb=" O PHE B2591 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B2596 " --> pdb=" O ARG B2592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2591 through 2596' Processing helix chain 'B' and resid 2601 through 2626 Processing helix chain 'B' and resid 2655 through 2660 Processing helix chain 'B' and resid 2671 through 2678 removed outlier: 4.074A pdb=" N MET B2678 " --> pdb=" O VAL B2674 " (cutoff:3.500A) Processing helix chain 'B' and resid 2685 through 2701 Processing helix chain 'B' and resid 2701 through 2715 Processing helix chain 'B' and resid 2723 through 2733 Processing helix chain 'B' and resid 2765 through 2778 removed outlier: 3.936A pdb=" N ARG B2769 " --> pdb=" O SER B2765 " (cutoff:3.500A) Processing helix chain 'B' and resid 2783 through 2797 Processing helix chain 'B' and resid 2797 through 2802 Processing sheet with id=AA1, first strand: chain 'A' and resid 2462 through 2467 removed outlier: 4.357A pdb=" N LYS A2476 " --> pdb=" O TRP A2533 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A2530 " --> pdb=" O ILE A2522 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2538 through 2539 removed outlier: 3.731A pdb=" N ILE A2538 " --> pdb=" O ILE A2638 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A2638 " --> pdb=" O ILE A2538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2404 through 2406 Processing sheet with id=AA4, first strand: chain 'B' and resid 2463 through 2467 Processing sheet with id=AA5, first strand: chain 'B' and resid 2538 through 2539 removed outlier: 3.659A pdb=" N ILE B2538 " --> pdb=" O ILE B2638 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B2638 " --> pdb=" O ILE B2538 " (cutoff:3.500A) 2146 hydrogen bonds defined for protein. 6363 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: 17.50 Time building geometry restraints manager: 10.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 11068 1.35 - 1.47: 7506 1.47 - 1.60: 13811 1.60 - 1.72: 6 1.72 - 1.85: 63 Bond restraints: 32454 Sorted by residual: bond pdb=" CA LYS A2658 " pdb=" C LYS A2658 " ideal model delta sigma weight residual 1.523 1.357 0.166 1.34e-02 5.57e+03 1.53e+02 bond pdb=" O3A ANP A2901 " pdb=" PB ANP A2901 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.15e+01 bond pdb=" O3A ANP B2901 " pdb=" PB ANP B2901 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" N3B ANP A2901 " pdb=" PG ANP A2901 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" N3B ANP B2901 " pdb=" PG ANP B2901 " ideal model delta sigma weight residual 1.795 1.694 0.101 2.00e-02 2.50e+03 2.57e+01 ... (remaining 32449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 44122 3.46 - 6.92: 229 6.92 - 10.38: 44 10.38 - 13.84: 12 13.84 - 17.31: 7 Bond angle restraints: 44414 Sorted by residual: angle pdb=" CA PRO A2334 " pdb=" N PRO A2334 " pdb=" CD PRO A2334 " ideal model delta sigma weight residual 112.00 98.20 13.80 1.40e+00 5.10e-01 9.72e+01 angle pdb=" CA GLY A2657 " pdb=" C GLY A2657 " pdb=" N LYS A2658 " ideal model delta sigma weight residual 116.69 101.54 15.15 2.04e+00 2.40e-01 5.52e+01 angle pdb=" N PRO A2661 " pdb=" CA PRO A2661 " pdb=" C PRO A2661 " ideal model delta sigma weight residual 113.53 103.89 9.64 1.39e+00 5.18e-01 4.80e+01 angle pdb=" CA PRO B2334 " pdb=" N PRO B2334 " pdb=" CD PRO B2334 " ideal model delta sigma weight residual 112.00 103.04 8.96 1.40e+00 5.10e-01 4.10e+01 angle pdb=" N GLY B2458 " pdb=" CA GLY B2458 " pdb=" C GLY B2458 " ideal model delta sigma weight residual 113.48 104.83 8.65 1.46e+00 4.69e-01 3.51e+01 ... (remaining 44409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.35: 17957 24.35 - 48.70: 1216 48.70 - 73.05: 160 73.05 - 97.40: 45 97.40 - 121.75: 1 Dihedral angle restraints: 19379 sinusoidal: 5000 harmonic: 14379 Sorted by residual: dihedral pdb=" C LYS A2563 " pdb=" N LYS A2563 " pdb=" CA LYS A2563 " pdb=" CB LYS A2563 " ideal model delta harmonic sigma weight residual -122.60 -141.60 19.00 0 2.50e+00 1.60e-01 5.78e+01 dihedral pdb=" CB CYS A2166 " pdb=" SG CYS A2166 " pdb=" SG CYS A2257 " pdb=" CB CYS A2257 " ideal model delta sinusoidal sigma weight residual -86.00 -20.11 -65.89 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" N LYS A2563 " pdb=" C LYS A2563 " pdb=" CA LYS A2563 " pdb=" CB LYS A2563 " ideal model delta harmonic sigma weight residual 122.80 138.59 -15.79 0 2.50e+00 1.60e-01 3.99e+01 ... (remaining 19376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 5469 0.124 - 0.249: 48 0.249 - 0.373: 4 0.373 - 0.497: 0 0.497 - 0.622: 1 Chirality restraints: 5522 Sorted by residual: chirality pdb=" CA LYS A2563 " pdb=" N LYS A2563 " pdb=" C LYS A2563 " pdb=" CB LYS A2563 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.66e+00 chirality pdb=" C3' ANP B2901 " pdb=" C2' ANP B2901 " pdb=" C4' ANP B2901 " pdb=" O3' ANP B2901 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA PRO B2334 " pdb=" N PRO B2334 " pdb=" C PRO B2334 " pdb=" CB PRO B2334 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 5519 not shown) Planarity restraints: 5830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A2657 " -0.066 2.00e-02 2.50e+03 1.40e-01 1.95e+02 pdb=" C GLY A2657 " 0.241 2.00e-02 2.50e+03 pdb=" O GLY A2657 " -0.101 2.00e-02 2.50e+03 pdb=" N LYS A2658 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A2333 " -0.112 5.00e-02 4.00e+02 1.57e-01 3.94e+01 pdb=" N PRO A2334 " 0.271 5.00e-02 4.00e+02 pdb=" CA PRO A2334 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO A2334 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A2561 " 0.024 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C CYS A2561 " -0.085 2.00e-02 2.50e+03 pdb=" O CYS A2561 " 0.032 2.00e-02 2.50e+03 pdb=" N ARG A2562 " 0.028 2.00e-02 2.50e+03 ... (remaining 5827 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 732 2.70 - 3.25: 35503 3.25 - 3.80: 53242 3.80 - 4.35: 62040 4.35 - 4.90: 97875 Nonbonded interactions: 249392 Sorted by model distance: nonbonded pdb=" O TYR B2192 " pdb=" N LYS B2196 " model vdw 2.148 3.120 nonbonded pdb=" O GLU A1825 " pdb=" ND2 ASN A1830 " model vdw 2.182 3.120 nonbonded pdb=" O LEU B 503 " pdb=" N SER B 507 " model vdw 2.186 3.120 nonbonded pdb=" O PHE B 385 " pdb=" N PHE B 389 " model vdw 2.196 3.120 nonbonded pdb=" O1B ANP B2901 " pdb=" O2G ANP B2901 " model vdw 2.213 3.040 ... (remaining 249387 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 'A' and (resid 98 through 159 or resid 161 through 297 or resid 299 throu \ gh 388 or resid 390 through 491 or resid 493 through 505 or resid 507 through 78 \ 8 or resid 791 through 901 or resid 903 through 993 or resid 996 through 1212 or \ (resid 1213 through 1216 and (name N or name CA or name C or name O or name CB \ )) or resid 1217 through 1219 or (resid 1220 and (name N or name CA or name C or \ name O or name CB )) or resid 1221 through 1254 or (resid 1255 through 1261 and \ (name N or name CA or name C or name O or name CB )) or resid 1262 through 1275 \ or (resid 1276 through 1277 and (name N or name CA or name C or name O or name \ CB )) or resid 1278 through 1279 or (resid 1280 through 1281 and (name N or name \ CA or name C or name O or name CB )) or resid 1282 through 1300 or (resid 1301 \ and (name N or name CA or name C or name O or name CB )) or resid 1302 through 1 \ 375 or (resid 1376 and (name N or name CA or name C or name O or name CB )) or r \ esid 1377 through 1378 or (resid 1379 through 1380 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1381 through 1382 or (resid 1383 through 13 \ 84 and (name N or name CA or name C or name O or name CB )) or resid 1385 throug \ h 1439 or (resid 1441 and (name N or name CA or name C or name O or name CB )) o \ r resid 1442 through 1485 or resid 1488 or (resid 1489 and (name N or name CA or \ name C or name O or name CB )) or resid 1490 through 1491 or (resid 1492 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1493 through 1494 or \ (resid 1495 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 496 through 1504 or (resid 1505 through 1506 and (name N or name CA or name C or \ name O or name CB )) or resid 1507 through 1508 or (resid 1509 through 1510 and \ (name N or name CA or name C or name O or name CB )) or resid 1511 through 1512 \ or (resid 1513 and (name N or name CA or name C or name O or name CB )) or resi \ d 1514 through 1537 or (resid 1538 and (name N or name CA or name C or name O or \ name CB )) or resid 1539 through 1565 or resid 1573 through 1577 or (resid 1578 \ and (name N or name CA or name C or name O or name CB )) or resid 1579 through \ 1586 or (resid 1587 through 1589 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1590 through 1595 or resid 1597 through 1599 or (resid 1600 t \ hrough 1601 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 02 through 1604 or (resid 1605 through 1606 and (name N or name CA or name C or \ name O or name CB )) or resid 1607 through 1609 or resid 1617 through 1623 or (r \ esid 1624 and (name N or name CA or name C or name O or name CB )) or resid 1625 \ through 1644 or (resid 1645 and (name N or name CA or name C or name O or name \ CB )) or resid 1646 through 1671 or (resid 1672 through 1674 and (name N or name \ CA or name C or name O or name CB )) or resid 1675 through 1679 or (resid 1681 \ through 1684 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 685 through 1691 or resid 1693 or (resid 1694 through 1696 and (name N or name C \ A or name C or name O or name CB )) or resid 1697 through 1750 or (resid 1751 an \ d (name N or name CA or name C or name O or name CB )) or resid 1752 through 176 \ 8 or (resid 1769 through 1771 and (name N or name CA or name C or name O or name \ CB )) or resid 1772 through 1868 or (resid 1869 and (name N or name CA or name \ C or name O or name CB )) or resid 1870 through 1882 or (resid 1883 and (name N \ or name CA or name C or name O or name CB )) or resid 1884 through 1896 or (resi \ d 1898 and (name N or name CA or name C or name O or name CB )) or resid 1899 th \ rough 1906 or (resid 1907 through 1908 and (name N or name CA or name C or name \ O or name CB )) or resid 1909 through 1928 or (resid 1929 and (name N or name CA \ or name C or name O or name CB )) or resid 1930 through 1933 or (resid 1934 and \ (name N or name CA or name C or name O or name CB )) or resid 1935 through 1945 \ or (resid 1946 and (name N or name CA or name C or name O or name CB )) or resi \ d 1947 through 1971 or (resid 1972 and (name N or name CA or name C or name O or \ name CB )) or resid 1973 through 1986 or resid 1989 through 2013 or resid 2015 \ through 2018 or resid 2020 through 2022 or (resid 2023 and (name N or name CA or \ name C or name O or name CB )) or resid 2024 through 2039 or (resid 2040 and (n \ ame N or name CA or name C or name O or name CB )) or resid 2042 through 2070 or \ (resid 2071 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 072 through 2085 or (resid 2086 and (name N or name CA or name C or name O or na \ me CB )) or resid 2087 through 2133 or (resid 2134 and (name N or name CA or nam \ e C or name O or name CB )) or resid 2135 through 2137 or (resid 2138 and (name \ N or name CA or name C or name O or name CB )) or resid 2139 through 2141 or res \ id 2143 through 2158 or (resid 2159 and (name N or name CA or name C or name O o \ r name CB )) or resid 2160 or (resid 2161 through 2163 and (name N or name CA or \ name C or name O or name CB )) or resid 2164 through 2165 or resid 2167 through \ 2169 or (resid 2170 through 2171 and (name N or name CA or name C or name O or \ name CB )) or resid 2172 through 2174 or (resid 2175 and (name N or name CA or n \ ame C or name O or name CB )) or resid 2176 through 2192 or (resid 2193 and (nam \ e N or name CA or name C or name O or name CB )) or resid 2194 through 2195 or r \ esid 2197 through 2220 or (resid 2221 through 2222 and (name N or name CA or nam \ e C or name O or name CB )) or resid 2223 or (resid 2224 and (name N or name CA \ or name C or name O or name CB )) or resid 2225 through 2228 or (resid 2229 and \ (name N or name CA or name C or name O or name CB )) or resid 2230 through 2246 \ or (resid 2247 through 2248 and (name N or name CA or name C or name O or name C \ B )) or resid 2249 or (resid 2250 and (name N or name CA or name C or name O or \ name CB )) or resid 2251 through 2252 or (resid 2253 and (name N or name CA or n \ ame C or name O or name CB )) or resid 2254 through 2256 or (resid 2257 and (nam \ e N or name CA or name C or name O or name CB )) or resid 2258 through 2259 or ( \ resid 2260 through 2262 and (name N or name CA or name C or name O or name CB )) \ or resid 2263 through 2294 or (resid 2295 and (name N or name CA or name C or n \ ame O or name CB )) or resid 2296 through 2298 or (resid 2299 and (name N or nam \ e CA or name C or name O or name CB )) or resid 2300 through 2315 or resid 2317 \ through 2319 or (resid 2320 and (name N or name CA or name C or name O or name C \ B )) or resid 2321 through 2324 or (resid 2325 through 2326 and (name N or name \ CA or name C or name O or name CB )) or resid 2327 through 2342 or (resid 2343 t \ hrough 2344 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 45 or (resid 2346 and (name N or name CA or name C or name O or name CB )) or re \ sid 2347 through 2383 or (resid 2384 through 2385 and (name N or name CA or name \ C or name O or name CB )) or resid 2386 through 2405 or (resid 2406 and (name N \ or name CA or name C or name O or name CB )) or resid 2407 through 2444 or (res \ id 2445 through 2446 and (name N or name CA or name C or name O or name CB )) or \ resid 2447 through 2469 or (resid 2470 and (name N or name CA or name C or name \ O or name CB )) or resid 2471 through 2486 or (resid 2487 through 2488 and (nam \ e N or name CA or name C or name O or name CB )) or resid 2489 through 2547 or ( \ resid 2548 and (name N or name CA or name C or name O or name CB )) or resid 254 \ 9 or (resid 2550 and (name N or name CA or name C or name O or name CB )) or res \ id 2551 through 2602 or (resid 2603 through 2604 and (name N or name CA or name \ C or name O or name CB )) or resid 2605 through 2606 or (resid 2607 through 2608 \ and (name N or name CA or name C or name O or name CB )) or resid 2609 through \ 2617 or (resid 2618 through 2621 and (name N or name CA or name C or name O or n \ ame CB )) or resid 2622 through 2687 or (resid 2688 and (name N or name CA or na \ me C or name O or name CB )) or resid 2689 through 2700 or (resid 2701 through 2 \ 703 and (name N or name CA or name C or name O or name CB )) or resid 2704 throu \ gh 2712 or (resid 2713 and (name N or name CA or name C or name O or name CB )) \ or resid 2714 through 2720 or (resid 2721 and (name N or name CA or name C or na \ me O or name CB )) or resid 2763 through 2809 or resid 2901)) selection = (chain 'B' and (resid 98 through 138 or resid 141 through 566 or resid 568 throu \ gh 1009 or resid 1014 through 1117 or resid 1124 through 1192 or (resid 1193 thr \ ough 1197 and (name N or name CA or name C or name O or name CB )) or resid 1198 \ through 1265 or (resid 1266 and (name N or name CA or name C or name O or name \ CB )) or resid 1267 through 1272 or (resid 1273 through 1274 and (name N or name \ CA or name C or name O or name CB )) or resid 1275 through 1290 or (resid 1291 \ through 1293 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 294 through 1320 or (resid 1321 and (name N or name CA or name C or name O or na \ me CB )) or resid 1322 through 1341 or (resid 1342 through 1347 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1348 through 1374 or (resid 13 \ 75 through 1376 and (name N or name CA or name C or name O or name CB )) or resi \ d 1377 through 1435 or (resid 1436 and (name N or name CA or name C or name O or \ name CB )) or resid 1437 through 1461 or (resid 1462 and (name N or name CA or \ name C or name O or name CB )) or resid 1463 through 1500 or (resid 1501 and (na \ me N or name CA or name C or name O or name CB )) or resid 1502 or (resid 1503 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1504 through 15 \ 26 or (resid 1527 and (name N or name CA or name C or name O or name CB )) or re \ sid 1528 through 1541 or (resid 1542 and (name N or name CA or name C or name O \ or name CB )) or resid 1543 through 1545 or (resid 1546 and (name N or name CA o \ r name C or name O or name CB )) or resid 1547 through 1556 or (resid 1557 and ( \ name N or name CA or name C or name O or name CB )) or resid 1558 through 1582 o \ r (resid 1583 and (name N or name CA or name C or name O or name CB )) or resid \ 1584 through 1602 or (resid 1603 through 1606 and (name N or name CA or name C o \ r name O or name CB )) or resid 1607 through 1635 or (resid 1638 and (name N or \ name CA or name C or name O or name CB )) or resid 1639 through 1657 or (resid 1 \ 658 and (name N or name CA or name C or name O or name CB )) or resid 1659 throu \ gh 1667 or (resid 1668 and (name N or name CA or name C or name O or name CB )) \ or resid 1669 through 1687 or (resid 1688 and (name N or name CA or name C or na \ me O or name CB )) or resid 1689 through 1690 or (resid 1691 and (name N or name \ CA or name C or name O or name CB )) or resid 1693 through 1697 or (resid 1698 \ through 1700 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 701 through 1738 or (resid 1739 and (name N or name CA or name C or name O or na \ me CB )) or resid 1740 or (resid 1741 through 1743 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1744 through 1764 or (resid 1765 and (name \ N or name CA or name C or name O or name CB )) or resid 1766 through 1776 or (re \ sid 1777 through 1778 and (name N or name CA or name C or name O or name CB )) o \ r resid 1779 through 1798 or (resid 1799 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1800 through 1806 or (resid 1807 and (name N or name \ CA or name C or name O or name CB )) or resid 1808 through 1833 or (resid 1834 t \ hrough 1835 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 36 through 1844 or (resid 1845 through 1847 and (name N or name CA or name C or \ name O or name CB )) or resid 1848 through 1870 or (resid 1871 and (name N or na \ me CA or name C or name O or name CB )) or resid 1872 through 1875 or (resid 187 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 1877 through \ 1921 or (resid 1922 and (name N or name CA or name C or name O or name CB )) or \ resid 1923 through 1930 or (resid 1931 through 1932 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1933 through 1935 or (resid 1936 through \ 1937 and (name N or name CA or name C or name O or name CB )) or resid 1938 thro \ ugh 1984 or (resid 1985 and (name N or name CA or name C or name O or name CB )) \ or resid 1986 through 1989 or (resid 1990 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1991 through 1995 or (resid 1996 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1997 through 2001 or (resid 2002 \ and (name N or name CA or name C or name O or name CB )) or resid 2003 through \ 2007 or (resid 2008 and (name N or name CA or name C or name O or name CB )) or \ resid 2009 through 2026 or (resid 2027 through 2028 and (name N or name CA or na \ me C or name O or name CB )) or resid 2029 through 2046 or (resid 2047 through 2 \ 048 and (name N or name CA or name C or name O or name CB )) or resid 2049 throu \ gh 2052 or (resid 2053 through 2054 and (name N or name CA or name C or name O o \ r name CB )) or resid 2055 through 2060 or (resid 2061 and (name N or name CA or \ name C or name O or name CB )) or resid 2062 through 2091 or (resid 2092 throug \ h 2093 and (name N or name CA or name C or name O or name CB )) or resid 2094 th \ rough 2122 or (resid 2123 through 2124 and (name N or name CA or name C or name \ O or name CB )) or resid 2125 through 2127 or (resid 2128 and (name N or name CA \ or name C or name O or name CB )) or resid 2129 through 2131 or (resid 2132 and \ (name N or name CA or name C or name O or name CB )) or resid 2133 through 2162 \ or (resid 2163 and (name N or name CA or name C or name O or name CB )) or resi \ d 2164 through 2165 or (resid 2167 and (name N or name CA or name C or name O or \ name CB )) or resid 2168 through 2179 or (resid 2180 and (name N or name CA or \ name C or name O or name CB )) or resid 2181 through 2182 or (resid 2183 and (na \ me N or name CA or name C or name O or name CB )) or resid 2184 through 2186 or \ (resid 2187 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 88 through 2198 or (resid 2199 and (name N or name CA or name C or name O or nam \ e CB )) or resid 2200 through 2221 or (resid 2222 and (name N or name CA or name \ C or name O or name CB )) or resid 2223 through 2226 or (resid 2227 and (name N \ or name CA or name C or name O or name CB )) or resid 2228 through 2234 or (res \ id 2235 and (name N or name CA or name C or name O or name CB )) or resid 2236 t \ hrough 2240 or (resid 2241 and (name N or name CA or name C or name O or name CB \ )) or resid 2242 through 2244 or (resid 2245 and (name N or name CA or name C o \ r name O or name CB )) or resid 2246 through 2247 or (resid 2248 and (name N or \ name CA or name C or name O or name CB )) or resid 2249 through 2276 or (resid 2 \ 277 and (name N or name CA or name C or name O or name CB )) or resid 2278 throu \ gh 2314 or (resid 2315 and (name N or name CA or name C or name O or name CB )) \ or resid 2317 through 2359 or (resid 2360 and (name N or name CA or name C or na \ me O or name CB )) or resid 2361 through 2363 or (resid 2364 and (name N or name \ CA or name C or name O or name CB )) or resid 2365 or (resid 2366 and (name N o \ r name CA or name C or name O or name CB )) or resid 2367 through 2369 or (resid \ 2370 through 2371 and (name N or name CA or name C or name O or name CB )) or r \ esid 2372 or (resid 2373 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 2377 through 2378 and (name N or name CA or name C or name O or name \ CB )) or resid 2379 through 2398 or (resid 2399 and (name N or name CA or name \ C or name O or name CB )) or resid 2400 through 2409 or (resid 2410 and (name N \ or name CA or name C or name O or name CB )) or resid 2411 through 2412 or (resi \ d 2413 and (name N or name CA or name C or name O or name CB )) or resid 2414 th \ rough 2445 or (resid 2446 and (name N or name CA or name C or name O or name CB \ )) or resid 2447 through 2448 or (resid 2449 and (name N or name CA or name C or \ name O or name CB )) or resid 2450 through 2462 or (resid 2463 and (name N or n \ ame CA or name C or name O or name CB )) or resid 2464 through 2487 or (resid 24 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 2489 throug \ h 2512 or (resid 2513 through 2514 and (name N or name CA or name C or name O or \ name CB )) or resid 2515 through 2534 or (resid 2535 and (name N or name CA or \ name C or name O or name CB )) or resid 2536 through 2566 or (resid 2567 and (na \ me N or name CA or name C or name O or name CB )) or resid 2568 through 2570 or \ (resid 2571 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 72 through 2586 or (resid 2587 through 2588 and (name N or name CA or name C or \ name O or name CB )) or resid 2589 through 2591 or (resid 2592 and (name N or na \ me CA or name C or name O or name CB )) or resid 2593 through 2603 or (resid 260 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 2605 through \ 2607 or (resid 2608 and (name N or name CA or name C or name O or name CB )) or \ resid 2609 through 2620 or (resid 2621 and (name N or name CA or name C or name \ O or name CB )) or resid 2622 through 2627 or (resid 2628 and (name N or name C \ A or name C or name O or name CB )) or resid 2629 through 2630 or (resid 2631 an \ d (name N or name CA or name C or name O or name CB )) or resid 2632 through 263 \ 4 or (resid 2635 and (name N or name CA or name C or name O or name CB )) or res \ id 2636 through 2643 or (resid 2644 and (name N or name CA or name C or name O o \ r name CB )) or resid 2645 through 2647 or (resid 2648 and (name N or name CA or \ name C or name O or name CB )) or resid 2649 or (resid 2650 and (name N or name \ CA or name C or name O or name CB )) or resid 2651 or (resid 2652 through 2653 \ and (name N or name CA or name C or name O or name CB )) or resid 2654 or (resid \ 2655 through 2656 and (name N or name CA or name C or name O or name CB )) or r \ esid 2657 through 2668 or (resid 2669 and (name N or name CA or name C or name O \ or name CB )) or resid 2670 through 2675 or (resid 2676 and (name N or name CA \ or name C or name O or name CB )) or resid 2677 or (resid 2678 and (name N or na \ me CA or name C or name O or name CB )) or resid 2679 through 2701 or (resid 270 \ 2 through 2703 and (name N or name CA or name C or name O or name CB )) or resid \ 2704 through 2706 or (resid 2707 through 2708 and (name N or name CA or name C \ or name O or name CB )) or resid 2709 through 2721 or resid 2763 through 2776 or \ (resid 2777 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 778 through 2809 or resid 2901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.040 Extract box with map and model: 1.200 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 83.050 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 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 : 0.004 0.166 32456 Z= 0.200 Angle : 0.732 17.306 44416 Z= 0.382 Chirality : 0.042 0.622 5522 Planarity : 0.005 0.157 5830 Dihedral : 17.038 121.747 9894 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.95 % Favored : 93.82 % Rotamer: Outliers : 1.29 % Allowed : 36.74 % Favored : 61.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4708 helix: 1.41 (0.10), residues: 3037 sheet: -1.20 (0.66), residues: 57 loop : -1.79 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1766 HIS 0.009 0.001 HIS B1394 PHE 0.039 0.001 PHE A2229 TYR 0.037 0.002 TYR A1276 ARG 0.003 0.000 ARG A1840 Details of bonding type rmsd hydrogen bonds : bond 0.12171 ( 2146) hydrogen bonds : angle 5.44365 ( 6363) SS BOND : bond 0.01207 ( 1) SS BOND : angle 6.14492 ( 2) covalent geometry : bond 0.00399 (32454) covalent geometry : angle 0.73100 (44414) Misc. bond : bond 0.00299 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 367 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2068 ASP cc_start: 0.6469 (OUTLIER) cc_final: 0.5973 (m-30) REVERT: A 2352 GLU cc_start: 0.8109 (mp0) cc_final: 0.7462 (pp20) REVERT: A 2430 MET cc_start: 0.5574 (mpp) cc_final: 0.4793 (mtm) REVERT: B 1543 MET cc_start: 0.7225 (mmt) cc_final: 0.6980 (mmt) REVERT: B 1944 HIS cc_start: 0.6898 (t-170) cc_final: 0.6544 (t-170) REVERT: B 2457 SER cc_start: 0.2755 (OUTLIER) cc_final: 0.2480 (m) REVERT: B 2729 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6985 (mtmm) REVERT: B 2732 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.5890 (mttt) outliers start: 29 outliers final: 12 residues processed: 387 average time/residue: 0.3746 time to fit residues: 248.3290 Evaluate side-chains 373 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 357 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1470 LYS Chi-restraints excluded: chain A residue 1935 ASN Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2068 ASP Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2348 VAL Chi-restraints excluded: chain A residue 2548 HIS Chi-restraints excluded: chain A residue 2637 LEU Chi-restraints excluded: chain B residue 1456 LEU Chi-restraints excluded: chain B residue 1599 LEU Chi-restraints excluded: chain B residue 1766 TRP Chi-restraints excluded: chain B residue 2457 SER Chi-restraints excluded: chain B residue 2485 ASP Chi-restraints excluded: chain B residue 2726 ARG Chi-restraints excluded: chain B residue 2729 LYS Chi-restraints excluded: chain B residue 2732 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 410 optimal weight: 0.0980 chunk 368 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 248 optimal weight: 50.0000 chunk 196 optimal weight: 2.9990 chunk 380 optimal weight: 0.0770 chunk 147 optimal weight: 1.9990 chunk 231 optimal weight: 0.0870 chunk 283 optimal weight: 5.9990 chunk 441 optimal weight: 9.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1830 ASN A2435 ASN A2454 HIS A2477 GLN ** B1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1759 ASN B1872 ASN B1879 ASN ** B1957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2373 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.185076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.146107 restraints weight = 69171.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.149964 restraints weight = 35438.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.152462 restraints weight = 22358.339| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 32456 Z= 0.116 Angle : 0.575 13.204 44416 Z= 0.296 Chirality : 0.039 0.220 5522 Planarity : 0.003 0.073 5830 Dihedral : 6.626 134.092 5091 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.29 % Favored : 94.54 % Rotamer: Outliers : 4.42 % Allowed : 32.19 % Favored : 63.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.13), residues: 4708 helix: 1.53 (0.09), residues: 3092 sheet: -0.96 (0.63), residues: 61 loop : -1.71 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1766 HIS 0.007 0.001 HIS A2339 PHE 0.041 0.001 PHE B1248 TYR 0.034 0.001 TYR B1205 ARG 0.007 0.000 ARG A1979 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 2146) hydrogen bonds : angle 4.44337 ( 6363) SS BOND : bond 0.00661 ( 1) SS BOND : angle 2.95747 ( 2) covalent geometry : bond 0.00234 (32454) covalent geometry : angle 0.57477 (44414) Misc. bond : bond 0.00217 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 391 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1250 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7838 (t80) REVERT: A 1268 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7058 (mp) REVERT: A 1358 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6724 (p0) REVERT: A 1736 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7661 (t0) REVERT: A 1751 ARG cc_start: 0.6223 (OUTLIER) cc_final: 0.5848 (mmm160) REVERT: A 2068 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: A 2202 LEU cc_start: 0.6939 (pp) cc_final: 0.6183 (tp) REVERT: A 2352 GLU cc_start: 0.7597 (mp0) cc_final: 0.7235 (pp20) REVERT: B 2047 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6813 (mt) REVERT: B 2131 TYR cc_start: 0.6975 (t80) cc_final: 0.6482 (t80) REVERT: B 2473 HIS cc_start: 0.5911 (t-90) cc_final: 0.5330 (p-80) REVERT: B 2729 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.6890 (mttt) outliers start: 99 outliers final: 42 residues processed: 468 average time/residue: 0.5443 time to fit residues: 441.0238 Evaluate side-chains 400 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 350 time to evaluate : 5.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1358 ASP Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1531 PHE Chi-restraints excluded: chain A residue 1736 ASN Chi-restraints excluded: chain A residue 1751 ARG Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1935 ASN Chi-restraints excluded: chain A residue 2015 ASN Chi-restraints excluded: chain A residue 2068 ASP Chi-restraints excluded: chain A residue 2150 LEU Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2348 VAL Chi-restraints excluded: chain A residue 2423 TYR Chi-restraints excluded: chain A residue 2548 HIS Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1456 LEU Chi-restraints excluded: chain B residue 1534 SER Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1759 ASN Chi-restraints excluded: chain B residue 1772 SER Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1822 ILE Chi-restraints excluded: chain B residue 1826 THR Chi-restraints excluded: chain B residue 1856 SER Chi-restraints excluded: chain B residue 1977 LEU Chi-restraints excluded: chain B residue 2009 LEU Chi-restraints excluded: chain B residue 2011 LEU Chi-restraints excluded: chain B residue 2047 ILE Chi-restraints excluded: chain B residue 2109 SER Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2428 ILE Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2645 VAL Chi-restraints excluded: chain B residue 2704 SER Chi-restraints excluded: chain B residue 2711 VAL Chi-restraints excluded: chain B residue 2729 LYS Chi-restraints excluded: chain B residue 2790 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 147 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 385 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 471 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 36 optimal weight: 50.0000 chunk 417 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1959 ASN ** B1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1957 ASN B2144 ASN B2373 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.170892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.141024 restraints weight = 69811.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.140396 restraints weight = 47460.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.141919 restraints weight = 37187.429| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32456 Z= 0.167 Angle : 0.620 14.519 44416 Z= 0.320 Chirality : 0.041 0.260 5522 Planarity : 0.004 0.053 5830 Dihedral : 5.946 124.981 5065 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.84 % Favored : 93.99 % Rotamer: Outliers : 6.25 % Allowed : 31.83 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.13), residues: 4708 helix: 1.52 (0.09), residues: 3079 sheet: -1.34 (0.62), residues: 61 loop : -1.77 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1766 HIS 0.006 0.001 HIS A2083 PHE 0.036 0.002 PHE B2074 TYR 0.022 0.002 TYR A1276 ARG 0.006 0.000 ARG A1979 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 2146) hydrogen bonds : angle 4.44989 ( 6363) SS BOND : bond 0.00776 ( 1) SS BOND : angle 1.50645 ( 2) covalent geometry : bond 0.00362 (32454) covalent geometry : angle 0.61993 (44414) Misc. bond : bond 0.00226 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 374 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1250 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7678 (t80) REVERT: A 1268 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6665 (mp) REVERT: A 1358 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7211 (p0) REVERT: A 1701 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7470 (pp) REVERT: A 2037 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5612 (tpm170) REVERT: A 2068 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7099 (m-30) REVERT: A 2202 LEU cc_start: 0.7306 (pp) cc_final: 0.6561 (tp) REVERT: A 2430 MET cc_start: 0.6280 (mpp) cc_final: 0.6069 (mpp) REVERT: B 1323 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8015 (mp) REVERT: B 1766 TRP cc_start: 0.6155 (OUTLIER) cc_final: 0.5663 (t60) REVERT: B 2047 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.6215 (mt) REVERT: B 2072 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6511 (mtm-85) REVERT: B 2107 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.7533 (m) REVERT: B 2275 TRP cc_start: 0.7497 (t60) cc_final: 0.7034 (t60) REVERT: B 2476 LYS cc_start: 0.6765 (OUTLIER) cc_final: 0.6475 (tttm) REVERT: B 2728 MET cc_start: 0.4410 (ttt) cc_final: 0.2474 (ptt) REVERT: B 2729 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6642 (mttt) outliers start: 140 outliers final: 75 residues processed: 481 average time/residue: 0.3725 time to fit residues: 308.6097 Evaluate side-chains 440 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 352 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1358 ASP Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1480 LEU Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1531 PHE Chi-restraints excluded: chain A residue 1558 HIS Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 SER Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1803 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1935 ASN Chi-restraints excluded: chain A residue 2015 ASN Chi-restraints excluded: chain A residue 2037 ARG Chi-restraints excluded: chain A residue 2068 ASP Chi-restraints excluded: chain A residue 2098 GLU Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2348 VAL Chi-restraints excluded: chain A residue 2423 TYR Chi-restraints excluded: chain A residue 2459 ILE Chi-restraints excluded: chain A residue 2510 SER Chi-restraints excluded: chain A residue 2530 VAL Chi-restraints excluded: chain A residue 2548 HIS Chi-restraints excluded: chain A residue 2568 LYS Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1456 LEU Chi-restraints excluded: chain B residue 1534 SER Chi-restraints excluded: chain B residue 1545 TRP Chi-restraints excluded: chain B residue 1592 LEU Chi-restraints excluded: chain B residue 1599 LEU Chi-restraints excluded: chain B residue 1698 ILE Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1739 ARG Chi-restraints excluded: chain B residue 1759 ASN Chi-restraints excluded: chain B residue 1766 TRP Chi-restraints excluded: chain B residue 1772 SER Chi-restraints excluded: chain B residue 1788 LEU Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1826 THR Chi-restraints excluded: chain B residue 1856 SER Chi-restraints excluded: chain B residue 1977 LEU Chi-restraints excluded: chain B residue 2011 LEU Chi-restraints excluded: chain B residue 2047 ILE Chi-restraints excluded: chain B residue 2072 ARG Chi-restraints excluded: chain B residue 2089 SER Chi-restraints excluded: chain B residue 2107 SER Chi-restraints excluded: chain B residue 2109 SER Chi-restraints excluded: chain B residue 2136 GLU Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2150 LEU Chi-restraints excluded: chain B residue 2251 ILE Chi-restraints excluded: chain B residue 2301 ILE Chi-restraints excluded: chain B residue 2351 ILE Chi-restraints excluded: chain B residue 2403 ASP Chi-restraints excluded: chain B residue 2428 ILE Chi-restraints excluded: chain B residue 2446 VAL Chi-restraints excluded: chain B residue 2474 THR Chi-restraints excluded: chain B residue 2476 LYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2645 VAL Chi-restraints excluded: chain B residue 2704 SER Chi-restraints excluded: chain B residue 2711 VAL Chi-restraints excluded: chain B residue 2726 ARG Chi-restraints excluded: chain B residue 2729 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 75 optimal weight: 30.0000 chunk 474 optimal weight: 4.9990 chunk 287 optimal weight: 0.0000 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 473 optimal weight: 0.9990 chunk 30 optimal weight: 40.0000 chunk 448 optimal weight: 9.9990 chunk 2 optimal weight: 50.0000 chunk 415 optimal weight: 2.9990 chunk 466 optimal weight: 0.5980 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2286 ASN ** B1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1759 ASN B2373 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.172595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.143059 restraints weight = 69626.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.143426 restraints weight = 45605.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.144394 restraints weight = 35466.982| |-----------------------------------------------------------------------------| r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32456 Z= 0.121 Angle : 0.591 14.190 44416 Z= 0.300 Chirality : 0.039 0.242 5522 Planarity : 0.003 0.054 5830 Dihedral : 5.583 121.180 5065 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.61 % Favored : 94.22 % Rotamer: Outliers : 5.98 % Allowed : 31.56 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.13), residues: 4708 helix: 1.59 (0.09), residues: 3091 sheet: -1.13 (0.63), residues: 61 loop : -1.77 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1766 HIS 0.007 0.001 HIS A2339 PHE 0.039 0.001 PHE B2074 TYR 0.032 0.001 TYR A1276 ARG 0.005 0.000 ARG B2359 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 2146) hydrogen bonds : angle 4.25506 ( 6363) SS BOND : bond 0.00726 ( 1) SS BOND : angle 0.57600 ( 2) covalent geometry : bond 0.00256 (32454) covalent geometry : angle 0.59109 (44414) Misc. bond : bond 0.00195 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 372 time to evaluate : 3.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1250 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7631 (t80) REVERT: A 1268 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6598 (mp) REVERT: A 1701 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7472 (pp) REVERT: A 1736 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7810 (t0) REVERT: A 1751 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.6191 (mmm160) REVERT: A 1945 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7240 (tt) REVERT: A 1987 CYS cc_start: 0.6510 (OUTLIER) cc_final: 0.6097 (p) REVERT: A 2003 LEU cc_start: 0.8058 (tt) cc_final: 0.7730 (tt) REVERT: A 2009 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5780 (tt) REVERT: A 2037 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5421 (tpm170) REVERT: A 2068 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: A 2202 LEU cc_start: 0.7339 (pp) cc_final: 0.6619 (tp) REVERT: A 2430 MET cc_start: 0.6350 (mpp) cc_final: 0.5929 (mpp) REVERT: A 2597 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6328 (pp20) REVERT: B 1239 VAL cc_start: 0.4877 (OUTLIER) cc_final: 0.4613 (p) REVERT: B 2047 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6639 (mt) REVERT: B 2072 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6264 (mtm-85) REVERT: B 2176 TYR cc_start: 0.8055 (t80) cc_final: 0.7795 (t80) REVERT: B 2275 TRP cc_start: 0.7483 (t60) cc_final: 0.7198 (t60) REVERT: B 2473 HIS cc_start: 0.6116 (t-90) cc_final: 0.5858 (p-80) REVERT: B 2728 MET cc_start: 0.4469 (ttt) cc_final: 0.2481 (ptt) REVERT: B 2729 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.6635 (mttt) outliers start: 134 outliers final: 81 residues processed: 479 average time/residue: 0.3743 time to fit residues: 308.6059 Evaluate side-chains 449 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 354 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1335 HIS Chi-restraints excluded: chain A residue 1360 PHE Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1470 LYS Chi-restraints excluded: chain A residue 1495 TYR Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1531 PHE Chi-restraints excluded: chain A residue 1558 HIS Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1736 ASN Chi-restraints excluded: chain A residue 1751 ARG Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1898 GLU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1935 ASN Chi-restraints excluded: chain A residue 1945 LEU Chi-restraints excluded: chain A residue 1954 LEU Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 1987 CYS Chi-restraints excluded: chain A residue 2009 LEU Chi-restraints excluded: chain A residue 2015 ASN Chi-restraints excluded: chain A residue 2037 ARG Chi-restraints excluded: chain A residue 2068 ASP Chi-restraints excluded: chain A residue 2098 GLU Chi-restraints excluded: chain A residue 2103 ILE Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2150 LEU Chi-restraints excluded: chain A residue 2153 MET Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2348 VAL Chi-restraints excluded: chain A residue 2423 TYR Chi-restraints excluded: chain A residue 2454 HIS Chi-restraints excluded: chain A residue 2510 SER Chi-restraints excluded: chain A residue 2524 LEU Chi-restraints excluded: chain A residue 2530 VAL Chi-restraints excluded: chain A residue 2548 HIS Chi-restraints excluded: chain A residue 2568 LYS Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2681 THR Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1534 SER Chi-restraints excluded: chain B residue 1545 TRP Chi-restraints excluded: chain B residue 1599 LEU Chi-restraints excluded: chain B residue 1698 ILE Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1772 SER Chi-restraints excluded: chain B residue 1788 LEU Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1822 ILE Chi-restraints excluded: chain B residue 1826 THR Chi-restraints excluded: chain B residue 1856 SER Chi-restraints excluded: chain B residue 1867 SER Chi-restraints excluded: chain B residue 2011 LEU Chi-restraints excluded: chain B residue 2047 ILE Chi-restraints excluded: chain B residue 2072 ARG Chi-restraints excluded: chain B residue 2103 ILE Chi-restraints excluded: chain B residue 2136 GLU Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2150 LEU Chi-restraints excluded: chain B residue 2251 ILE Chi-restraints excluded: chain B residue 2351 ILE Chi-restraints excluded: chain B residue 2403 ASP Chi-restraints excluded: chain B residue 2428 ILE Chi-restraints excluded: chain B residue 2446 VAL Chi-restraints excluded: chain B residue 2459 ILE Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2645 VAL Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2704 SER Chi-restraints excluded: chain B residue 2711 VAL Chi-restraints excluded: chain B residue 2726 ARG Chi-restraints excluded: chain B residue 2729 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 53 optimal weight: 50.0000 chunk 298 optimal weight: 30.0000 chunk 435 optimal weight: 0.7980 chunk 216 optimal weight: 0.9990 chunk 186 optimal weight: 0.5980 chunk 294 optimal weight: 30.0000 chunk 94 optimal weight: 40.0000 chunk 35 optimal weight: 8.9990 chunk 389 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1959 ASN ** B1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2144 ASN B2373 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.171779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.142750 restraints weight = 69624.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.142129 restraints weight = 47600.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.143701 restraints weight = 34958.009| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32456 Z= 0.145 Angle : 0.610 13.837 44416 Z= 0.312 Chirality : 0.040 0.243 5522 Planarity : 0.003 0.052 5830 Dihedral : 5.512 120.250 5063 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.73 % Favored : 94.07 % Rotamer: Outliers : 6.21 % Allowed : 32.23 % Favored : 61.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.13), residues: 4708 helix: 1.58 (0.09), residues: 3092 sheet: -1.31 (0.63), residues: 61 loop : -1.84 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1766 HIS 0.007 0.001 HIS A2339 PHE 0.032 0.001 PHE A2229 TYR 0.036 0.002 TYR B1435 ARG 0.005 0.000 ARG B2359 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 2146) hydrogen bonds : angle 4.27840 ( 6363) SS BOND : bond 0.00966 ( 1) SS BOND : angle 5.17283 ( 2) covalent geometry : bond 0.00316 (32454) covalent geometry : angle 0.60949 (44414) Misc. bond : bond 0.00210 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 374 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1250 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7607 (t80) REVERT: A 1268 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6667 (mp) REVERT: A 1701 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7498 (pp) REVERT: A 1736 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7829 (t0) REVERT: A 1751 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.6129 (mmm160) REVERT: A 1987 CYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6039 (p) REVERT: A 2009 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5858 (tt) REVERT: A 2033 LEU cc_start: 0.6091 (tp) cc_final: 0.5849 (tt) REVERT: A 2037 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5447 (tpm170) REVERT: A 2068 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: A 2165 TYR cc_start: 0.7008 (m-80) cc_final: 0.6700 (m-80) REVERT: A 2202 LEU cc_start: 0.7263 (pp) cc_final: 0.6520 (tp) REVERT: A 2430 MET cc_start: 0.6486 (mpp) cc_final: 0.6073 (mpp) REVERT: A 2597 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6525 (pp20) REVERT: B 1239 VAL cc_start: 0.4937 (OUTLIER) cc_final: 0.4664 (p) REVERT: B 1766 TRP cc_start: 0.6184 (OUTLIER) cc_final: 0.5618 (t60) REVERT: B 2047 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6550 (mt) REVERT: B 2072 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6251 (mtm-85) REVERT: B 2176 TYR cc_start: 0.8015 (t80) cc_final: 0.7809 (t80) REVERT: B 2275 TRP cc_start: 0.7618 (t60) cc_final: 0.7266 (t60) REVERT: B 2288 LEU cc_start: 0.6344 (pp) cc_final: 0.6086 (pp) REVERT: B 2476 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6650 (tttm) REVERT: B 2728 MET cc_start: 0.4518 (ttt) cc_final: 0.2506 (ptt) REVERT: B 2729 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6602 (mttt) outliers start: 139 outliers final: 101 residues processed: 483 average time/residue: 0.3701 time to fit residues: 307.8977 Evaluate side-chains 474 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 358 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1335 HIS Chi-restraints excluded: chain A residue 1360 PHE Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1470 LYS Chi-restraints excluded: chain A residue 1495 TYR Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1531 PHE Chi-restraints excluded: chain A residue 1558 HIS Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1684 LYS Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1736 ASN Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1751 ARG Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1803 ILE Chi-restraints excluded: chain A residue 1898 GLU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1935 ASN Chi-restraints excluded: chain A residue 1954 LEU Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 1987 CYS Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2009 LEU Chi-restraints excluded: chain A residue 2015 ASN Chi-restraints excluded: chain A residue 2037 ARG Chi-restraints excluded: chain A residue 2068 ASP Chi-restraints excluded: chain A residue 2098 GLU Chi-restraints excluded: chain A residue 2103 ILE Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2153 MET Chi-restraints excluded: chain A residue 2189 GLU Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2348 VAL Chi-restraints excluded: chain A residue 2423 TYR Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2498 GLN Chi-restraints excluded: chain A residue 2510 SER Chi-restraints excluded: chain A residue 2530 VAL Chi-restraints excluded: chain A residue 2548 HIS Chi-restraints excluded: chain A residue 2568 LYS Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2681 THR Chi-restraints excluded: chain A residue 2698 LEU Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1456 LEU Chi-restraints excluded: chain B residue 1476 VAL Chi-restraints excluded: chain B residue 1534 SER Chi-restraints excluded: chain B residue 1545 TRP Chi-restraints excluded: chain B residue 1548 PHE Chi-restraints excluded: chain B residue 1553 ILE Chi-restraints excluded: chain B residue 1599 LEU Chi-restraints excluded: chain B residue 1698 ILE Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1735 THR Chi-restraints excluded: chain B residue 1759 ASN Chi-restraints excluded: chain B residue 1766 TRP Chi-restraints excluded: chain B residue 1772 SER Chi-restraints excluded: chain B residue 1788 LEU Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1817 ASP Chi-restraints excluded: chain B residue 1826 THR Chi-restraints excluded: chain B residue 1856 SER Chi-restraints excluded: chain B residue 1867 SER Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 1977 LEU Chi-restraints excluded: chain B residue 2011 LEU Chi-restraints excluded: chain B residue 2047 ILE Chi-restraints excluded: chain B residue 2072 ARG Chi-restraints excluded: chain B residue 2103 ILE Chi-restraints excluded: chain B residue 2109 SER Chi-restraints excluded: chain B residue 2136 GLU Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2150 LEU Chi-restraints excluded: chain B residue 2251 ILE Chi-restraints excluded: chain B residue 2301 ILE Chi-restraints excluded: chain B residue 2313 ASN Chi-restraints excluded: chain B residue 2351 ILE Chi-restraints excluded: chain B residue 2403 ASP Chi-restraints excluded: chain B residue 2428 ILE Chi-restraints excluded: chain B residue 2446 VAL Chi-restraints excluded: chain B residue 2459 ILE Chi-restraints excluded: chain B residue 2465 ILE Chi-restraints excluded: chain B residue 2476 LYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2645 VAL Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2704 SER Chi-restraints excluded: chain B residue 2711 VAL Chi-restraints excluded: chain B residue 2726 ARG Chi-restraints excluded: chain B residue 2729 LYS Chi-restraints excluded: chain B residue 2781 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 227 optimal weight: 0.7980 chunk 314 optimal weight: 30.0000 chunk 206 optimal weight: 0.0370 chunk 375 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 441 optimal weight: 2.9990 chunk 389 optimal weight: 0.7980 chunk 369 optimal weight: 0.0070 chunk 83 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.175395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.147268 restraints weight = 70470.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.146627 restraints weight = 48991.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.148044 restraints weight = 39725.627| |-----------------------------------------------------------------------------| r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32456 Z= 0.110 Angle : 0.588 14.530 44416 Z= 0.294 Chirality : 0.039 0.235 5522 Planarity : 0.003 0.053 5830 Dihedral : 5.307 123.257 5063 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.40 % Favored : 94.48 % Rotamer: Outliers : 6.25 % Allowed : 32.59 % Favored : 61.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.13), residues: 4708 helix: 1.74 (0.10), residues: 3084 sheet: -1.09 (0.64), residues: 61 loop : -1.78 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1766 HIS 0.007 0.001 HIS A2339 PHE 0.032 0.001 PHE B2342 TYR 0.036 0.001 TYR B1435 ARG 0.006 0.000 ARG B2310 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 2146) hydrogen bonds : angle 4.08704 ( 6363) SS BOND : bond 0.01127 ( 1) SS BOND : angle 3.45136 ( 2) covalent geometry : bond 0.00227 (32454) covalent geometry : angle 0.58708 (44414) Misc. bond : bond 0.00161 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 376 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1250 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7663 (t80) REVERT: A 1268 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6714 (mp) REVERT: A 1643 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6928 (pp20) REVERT: A 1684 LYS cc_start: 0.6348 (OUTLIER) cc_final: 0.5710 (mmtt) REVERT: A 1701 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7582 (pt) REVERT: A 1731 LEU cc_start: 0.5533 (OUTLIER) cc_final: 0.5249 (mm) REVERT: A 1736 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7817 (t0) REVERT: A 1751 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.6038 (mmm160) REVERT: A 1987 CYS cc_start: 0.6507 (OUTLIER) cc_final: 0.6213 (t) REVERT: A 2005 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6826 (pm20) REVERT: A 2037 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.5238 (tpm170) REVERT: A 2038 LYS cc_start: 0.6638 (OUTLIER) cc_final: 0.6154 (ttmm) REVERT: A 2068 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6930 (m-30) REVERT: A 2076 LEU cc_start: 0.7065 (mp) cc_final: 0.6768 (mp) REVERT: A 2202 LEU cc_start: 0.7363 (pp) cc_final: 0.6695 (tp) REVERT: A 2430 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.6005 (mpp) REVERT: A 2597 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6393 (pp20) REVERT: A 2713 ARG cc_start: 0.7023 (mtm180) cc_final: 0.6727 (mtm180) REVERT: B 1766 TRP cc_start: 0.6117 (OUTLIER) cc_final: 0.5544 (t60) REVERT: B 2072 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6918 (mmp80) REVERT: B 2476 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6646 (tttm) REVERT: B 2624 HIS cc_start: 0.6710 (t-170) cc_final: 0.6463 (t70) REVERT: B 2728 MET cc_start: 0.4500 (ttt) cc_final: 0.2504 (ptt) REVERT: B 2729 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6651 (mttt) outliers start: 140 outliers final: 91 residues processed: 487 average time/residue: 0.4012 time to fit residues: 333.3650 Evaluate side-chains 461 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 352 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1335 HIS Chi-restraints excluded: chain A residue 1360 PHE Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1470 LYS Chi-restraints excluded: chain A residue 1495 TYR Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1531 PHE Chi-restraints excluded: chain A residue 1558 HIS Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1643 GLU Chi-restraints excluded: chain A residue 1684 LYS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1736 ASN Chi-restraints excluded: chain A residue 1751 ARG Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1935 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 1987 CYS Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2015 ASN Chi-restraints excluded: chain A residue 2037 ARG Chi-restraints excluded: chain A residue 2038 LYS Chi-restraints excluded: chain A residue 2068 ASP Chi-restraints excluded: chain A residue 2098 GLU Chi-restraints excluded: chain A residue 2103 ILE Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2150 LEU Chi-restraints excluded: chain A residue 2153 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2348 VAL Chi-restraints excluded: chain A residue 2423 TYR Chi-restraints excluded: chain A residue 2430 MET Chi-restraints excluded: chain A residue 2454 HIS Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2510 SER Chi-restraints excluded: chain A residue 2524 LEU Chi-restraints excluded: chain A residue 2530 VAL Chi-restraints excluded: chain A residue 2548 HIS Chi-restraints excluded: chain A residue 2568 LYS Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2696 GLU Chi-restraints excluded: chain A residue 2788 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1323 ILE Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1456 LEU Chi-restraints excluded: chain B residue 1534 SER Chi-restraints excluded: chain B residue 1545 TRP Chi-restraints excluded: chain B residue 1548 PHE Chi-restraints excluded: chain B residue 1553 ILE Chi-restraints excluded: chain B residue 1599 LEU Chi-restraints excluded: chain B residue 1698 ILE Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1759 ASN Chi-restraints excluded: chain B residue 1766 TRP Chi-restraints excluded: chain B residue 1788 LEU Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1822 ILE Chi-restraints excluded: chain B residue 1826 THR Chi-restraints excluded: chain B residue 1867 SER Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 1977 LEU Chi-restraints excluded: chain B residue 2009 LEU Chi-restraints excluded: chain B residue 2011 LEU Chi-restraints excluded: chain B residue 2035 SER Chi-restraints excluded: chain B residue 2072 ARG Chi-restraints excluded: chain B residue 2103 ILE Chi-restraints excluded: chain B residue 2136 GLU Chi-restraints excluded: chain B residue 2150 LEU Chi-restraints excluded: chain B residue 2251 ILE Chi-restraints excluded: chain B residue 2313 ASN Chi-restraints excluded: chain B residue 2351 ILE Chi-restraints excluded: chain B residue 2403 ASP Chi-restraints excluded: chain B residue 2428 ILE Chi-restraints excluded: chain B residue 2446 VAL Chi-restraints excluded: chain B residue 2459 ILE Chi-restraints excluded: chain B residue 2465 ILE Chi-restraints excluded: chain B residue 2474 THR Chi-restraints excluded: chain B residue 2476 LYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2565 ILE Chi-restraints excluded: chain B residue 2645 VAL Chi-restraints excluded: chain B residue 2652 ILE Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2704 SER Chi-restraints excluded: chain B residue 2711 VAL Chi-restraints excluded: chain B residue 2729 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 138 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 10 optimal weight: 40.0000 chunk 103 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 240 optimal weight: 0.9980 chunk 319 optimal weight: 50.0000 chunk 448 optimal weight: 20.0000 chunk 310 optimal weight: 5.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1959 ASN A2059 ASN ** B1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2144 ASN B2278 ASN ** B2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2373 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.168852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.139561 restraints weight = 70098.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.139012 restraints weight = 47652.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.140403 restraints weight = 37950.088| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32456 Z= 0.202 Angle : 0.678 13.778 44416 Z= 0.349 Chirality : 0.042 0.198 5522 Planarity : 0.004 0.057 5830 Dihedral : 5.593 122.536 5063 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.29 % Favored : 93.61 % Rotamer: Outliers : 6.52 % Allowed : 32.59 % Favored : 60.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.13), residues: 4708 helix: 1.47 (0.09), residues: 3082 sheet: -1.83 (0.59), residues: 63 loop : -1.87 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B2275 HIS 0.007 0.001 HIS A2083 PHE 0.052 0.002 PHE A2229 TYR 0.043 0.002 TYR B2360 ARG 0.008 0.001 ARG A2672 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 2146) hydrogen bonds : angle 4.41489 ( 6363) SS BOND : bond 0.01102 ( 1) SS BOND : angle 2.42043 ( 2) covalent geometry : bond 0.00450 (32454) covalent geometry : angle 0.67794 (44414) Misc. bond : bond 0.00256 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 363 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1250 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7602 (t80) REVERT: A 1268 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6729 (mp) REVERT: A 1701 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7533 (pp) REVERT: A 1731 LEU cc_start: 0.5271 (OUTLIER) cc_final: 0.4976 (mm) REVERT: A 1987 CYS cc_start: 0.6463 (OUTLIER) cc_final: 0.6169 (t) REVERT: A 2037 ARG cc_start: 0.6361 (OUTLIER) cc_final: 0.5840 (tpm170) REVERT: A 2068 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: A 2202 LEU cc_start: 0.7293 (pp) cc_final: 0.6508 (tp) REVERT: A 2430 MET cc_start: 0.6494 (OUTLIER) cc_final: 0.6170 (mpp) REVERT: A 2440 TYR cc_start: 0.3442 (OUTLIER) cc_final: 0.0724 (p90) REVERT: A 2597 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6630 (pp20) REVERT: B 1239 VAL cc_start: 0.4921 (OUTLIER) cc_final: 0.4659 (p) REVERT: B 1766 TRP cc_start: 0.6282 (OUTLIER) cc_final: 0.5709 (t60) REVERT: B 2072 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6319 (mtm-85) REVERT: B 2107 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.7645 (m) REVERT: B 2728 MET cc_start: 0.4616 (ttt) cc_final: 0.2593 (ptt) REVERT: B 2729 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.6622 (mttt) REVERT: B 2733 MET cc_start: 0.5507 (mmp) cc_final: 0.5178 (mmm) outliers start: 146 outliers final: 108 residues processed: 480 average time/residue: 0.3945 time to fit residues: 328.0321 Evaluate side-chains 475 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 353 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1335 HIS Chi-restraints excluded: chain A residue 1360 PHE Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1470 LYS Chi-restraints excluded: chain A residue 1495 TYR Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1531 PHE Chi-restraints excluded: chain A residue 1558 HIS Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 SER Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1684 LYS Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1717 LYS Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1803 ILE Chi-restraints excluded: chain A residue 1898 GLU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1935 ASN Chi-restraints excluded: chain A residue 1954 LEU Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 1987 CYS Chi-restraints excluded: chain A residue 2000 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2015 ASN Chi-restraints excluded: chain A residue 2037 ARG Chi-restraints excluded: chain A residue 2045 LEU Chi-restraints excluded: chain A residue 2068 ASP Chi-restraints excluded: chain A residue 2098 GLU Chi-restraints excluded: chain A residue 2103 ILE Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2153 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2348 VAL Chi-restraints excluded: chain A residue 2423 TYR Chi-restraints excluded: chain A residue 2430 MET Chi-restraints excluded: chain A residue 2440 TYR Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2510 SER Chi-restraints excluded: chain A residue 2530 VAL Chi-restraints excluded: chain A residue 2548 HIS Chi-restraints excluded: chain A residue 2568 LYS Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2681 THR Chi-restraints excluded: chain A residue 2696 GLU Chi-restraints excluded: chain A residue 2704 SER Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain A residue 2788 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1456 LEU Chi-restraints excluded: chain B residue 1534 SER Chi-restraints excluded: chain B residue 1545 TRP Chi-restraints excluded: chain B residue 1548 PHE Chi-restraints excluded: chain B residue 1553 ILE Chi-restraints excluded: chain B residue 1599 LEU Chi-restraints excluded: chain B residue 1697 ILE Chi-restraints excluded: chain B residue 1698 ILE Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1735 THR Chi-restraints excluded: chain B residue 1739 ARG Chi-restraints excluded: chain B residue 1759 ASN Chi-restraints excluded: chain B residue 1766 TRP Chi-restraints excluded: chain B residue 1772 SER Chi-restraints excluded: chain B residue 1788 LEU Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1817 ASP Chi-restraints excluded: chain B residue 1826 THR Chi-restraints excluded: chain B residue 1856 SER Chi-restraints excluded: chain B residue 1867 SER Chi-restraints excluded: chain B residue 1920 THR Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 1977 LEU Chi-restraints excluded: chain B residue 2011 LEU Chi-restraints excluded: chain B residue 2035 SER Chi-restraints excluded: chain B residue 2072 ARG Chi-restraints excluded: chain B residue 2089 SER Chi-restraints excluded: chain B residue 2103 ILE Chi-restraints excluded: chain B residue 2107 SER Chi-restraints excluded: chain B residue 2109 SER Chi-restraints excluded: chain B residue 2136 GLU Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2150 LEU Chi-restraints excluded: chain B residue 2237 LEU Chi-restraints excluded: chain B residue 2251 ILE Chi-restraints excluded: chain B residue 2301 ILE Chi-restraints excluded: chain B residue 2313 ASN Chi-restraints excluded: chain B residue 2351 ILE Chi-restraints excluded: chain B residue 2403 ASP Chi-restraints excluded: chain B residue 2428 ILE Chi-restraints excluded: chain B residue 2446 VAL Chi-restraints excluded: chain B residue 2459 ILE Chi-restraints excluded: chain B residue 2465 ILE Chi-restraints excluded: chain B residue 2474 THR Chi-restraints excluded: chain B residue 2524 LEU Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2645 VAL Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2704 SER Chi-restraints excluded: chain B residue 2711 VAL Chi-restraints excluded: chain B residue 2729 LYS Chi-restraints excluded: chain B residue 2781 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 47 optimal weight: 30.0000 chunk 434 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 281 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 453 optimal weight: 0.0770 chunk 343 optimal weight: 0.0470 chunk 355 optimal weight: 5.9990 chunk 30 optimal weight: 50.0000 chunk 223 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1513 HIS ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1755 HIS B2059 ASN B2373 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.171286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.142102 restraints weight = 69534.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.142497 restraints weight = 46731.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.143486 restraints weight = 34472.540| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32456 Z= 0.139 Angle : 0.627 13.459 44416 Z= 0.317 Chirality : 0.040 0.215 5522 Planarity : 0.003 0.057 5830 Dihedral : 5.489 124.056 5063 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.01 % Favored : 93.88 % Rotamer: Outliers : 5.62 % Allowed : 33.75 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.13), residues: 4708 helix: 1.57 (0.10), residues: 3078 sheet: -1.86 (0.58), residues: 63 loop : -1.84 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B2275 HIS 0.007 0.001 HIS A2083 PHE 0.052 0.001 PHE A2229 TYR 0.034 0.002 TYR A1276 ARG 0.005 0.000 ARG A2700 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 2146) hydrogen bonds : angle 4.25635 ( 6363) SS BOND : bond 0.00971 ( 1) SS BOND : angle 1.74251 ( 2) covalent geometry : bond 0.00303 (32454) covalent geometry : angle 0.62714 (44414) Misc. bond : bond 0.00209 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 366 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1250 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7623 (t80) REVERT: A 1268 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6831 (mp) REVERT: A 1643 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6720 (pp20) REVERT: A 1701 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7487 (pp) REVERT: A 1731 LEU cc_start: 0.5402 (OUTLIER) cc_final: 0.5108 (mm) REVERT: A 1736 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7948 (t0) REVERT: A 1751 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.6025 (mmm160) REVERT: A 1987 CYS cc_start: 0.6444 (OUTLIER) cc_final: 0.6168 (t) REVERT: A 2033 LEU cc_start: 0.5897 (tp) cc_final: 0.5658 (tt) REVERT: A 2037 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5539 (tpm170) REVERT: A 2068 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: A 2202 LEU cc_start: 0.7318 (pp) cc_final: 0.6604 (tp) REVERT: A 2430 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.6120 (mpp) REVERT: A 2476 LYS cc_start: 0.6114 (OUTLIER) cc_final: 0.5468 (mtmm) REVERT: A 2597 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6485 (pp20) REVERT: B 1239 VAL cc_start: 0.4928 (OUTLIER) cc_final: 0.4670 (p) REVERT: B 1766 TRP cc_start: 0.6266 (OUTLIER) cc_final: 0.5736 (t60) REVERT: B 2072 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6231 (mtm-85) REVERT: B 2728 MET cc_start: 0.4453 (ttt) cc_final: 0.2584 (ptt) REVERT: B 2729 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.6728 (mttt) REVERT: B 2733 MET cc_start: 0.5523 (mmp) cc_final: 0.5147 (mmm) outliers start: 126 outliers final: 99 residues processed: 466 average time/residue: 0.3940 time to fit residues: 314.7473 Evaluate side-chains 470 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 355 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1335 HIS Chi-restraints excluded: chain A residue 1360 PHE Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1470 LYS Chi-restraints excluded: chain A residue 1495 TYR Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1531 PHE Chi-restraints excluded: chain A residue 1558 HIS Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 SER Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1631 ILE Chi-restraints excluded: chain A residue 1643 GLU Chi-restraints excluded: chain A residue 1684 LYS Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1717 LYS Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1736 ASN Chi-restraints excluded: chain A residue 1751 ARG Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1898 GLU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1954 LEU Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 1987 CYS Chi-restraints excluded: chain A residue 2000 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2015 ASN Chi-restraints excluded: chain A residue 2037 ARG Chi-restraints excluded: chain A residue 2068 ASP Chi-restraints excluded: chain A residue 2098 GLU Chi-restraints excluded: chain A residue 2103 ILE Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2153 MET Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2348 VAL Chi-restraints excluded: chain A residue 2423 TYR Chi-restraints excluded: chain A residue 2430 MET Chi-restraints excluded: chain A residue 2454 HIS Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2510 SER Chi-restraints excluded: chain A residue 2530 VAL Chi-restraints excluded: chain A residue 2548 HIS Chi-restraints excluded: chain A residue 2568 LYS Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2681 THR Chi-restraints excluded: chain A residue 2696 GLU Chi-restraints excluded: chain A residue 2788 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1456 LEU Chi-restraints excluded: chain B residue 1534 SER Chi-restraints excluded: chain B residue 1545 TRP Chi-restraints excluded: chain B residue 1548 PHE Chi-restraints excluded: chain B residue 1553 ILE Chi-restraints excluded: chain B residue 1599 LEU Chi-restraints excluded: chain B residue 1697 ILE Chi-restraints excluded: chain B residue 1698 ILE Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1735 THR Chi-restraints excluded: chain B residue 1759 ASN Chi-restraints excluded: chain B residue 1766 TRP Chi-restraints excluded: chain B residue 1772 SER Chi-restraints excluded: chain B residue 1788 LEU Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1826 THR Chi-restraints excluded: chain B residue 1856 SER Chi-restraints excluded: chain B residue 1867 SER Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 2011 LEU Chi-restraints excluded: chain B residue 2072 ARG Chi-restraints excluded: chain B residue 2103 ILE Chi-restraints excluded: chain B residue 2136 GLU Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2150 LEU Chi-restraints excluded: chain B residue 2241 THR Chi-restraints excluded: chain B residue 2251 ILE Chi-restraints excluded: chain B residue 2313 ASN Chi-restraints excluded: chain B residue 2351 ILE Chi-restraints excluded: chain B residue 2403 ASP Chi-restraints excluded: chain B residue 2428 ILE Chi-restraints excluded: chain B residue 2446 VAL Chi-restraints excluded: chain B residue 2459 ILE Chi-restraints excluded: chain B residue 2465 ILE Chi-restraints excluded: chain B residue 2474 THR Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2645 VAL Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2704 SER Chi-restraints excluded: chain B residue 2711 VAL Chi-restraints excluded: chain B residue 2729 LYS Chi-restraints excluded: chain B residue 2781 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 154 optimal weight: 6.9990 chunk 413 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 373 optimal weight: 6.9990 chunk 448 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 25 optimal weight: 40.0000 chunk 38 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 280 optimal weight: 8.9990 chunk 327 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1852 ASN A1959 ASN A2285 ASN A2422 ASN A2586 HIS B1343 GLN ** B1394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2024 HIS B2144 ASN ** B2373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.165072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.126879 restraints weight = 70373.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.128935 restraints weight = 42939.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.129355 restraints weight = 32122.174| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 32456 Z= 0.310 Angle : 0.818 13.948 44416 Z= 0.427 Chirality : 0.047 0.254 5522 Planarity : 0.005 0.055 5830 Dihedral : 6.169 121.903 5061 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.67 % Rotamer: Outliers : 6.34 % Allowed : 33.35 % Favored : 60.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 4708 helix: 0.87 (0.09), residues: 3070 sheet: -2.41 (0.62), residues: 51 loop : -2.12 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B2275 HIS 0.011 0.002 HIS B1394 PHE 0.052 0.003 PHE A2229 TYR 0.047 0.003 TYR A2039 ARG 0.009 0.001 ARG B2037 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 2146) hydrogen bonds : angle 4.96877 ( 6363) SS BOND : bond 0.01548 ( 1) SS BOND : angle 2.09773 ( 2) covalent geometry : bond 0.00686 (32454) covalent geometry : angle 0.81758 (44414) Misc. bond : bond 0.00337 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 369 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1250 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7856 (t80) REVERT: A 1731 LEU cc_start: 0.4692 (OUTLIER) cc_final: 0.4392 (mm) REVERT: A 1736 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7836 (t0) REVERT: A 1987 CYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6478 (p) REVERT: A 2173 ASP cc_start: 0.7299 (t0) cc_final: 0.7048 (t0) REVERT: A 2430 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6699 (mpp) REVERT: A 2440 TYR cc_start: 0.3280 (OUTLIER) cc_final: 0.0173 (p90) REVERT: A 2476 LYS cc_start: 0.6176 (OUTLIER) cc_final: 0.5513 (mtmm) REVERT: A 2632 HIS cc_start: 0.6970 (t-90) cc_final: 0.6632 (t-90) REVERT: B 1239 VAL cc_start: 0.5131 (OUTLIER) cc_final: 0.4865 (p) REVERT: B 1543 MET cc_start: 0.7583 (mmt) cc_final: 0.6897 (mmt) REVERT: B 1766 TRP cc_start: 0.6257 (OUTLIER) cc_final: 0.5811 (t60) REVERT: B 1848 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7739 (mm) REVERT: B 2072 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6533 (mtm-85) REVERT: B 2275 TRP cc_start: 0.7779 (t60) cc_final: 0.7280 (t60) REVERT: B 2655 GLU cc_start: 0.6578 (tm-30) cc_final: 0.6369 (tm-30) REVERT: B 2684 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: B 2728 MET cc_start: 0.4252 (ttt) cc_final: 0.2498 (ptt) REVERT: B 2729 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.6615 (mttt) REVERT: B 2733 MET cc_start: 0.6053 (mmp) cc_final: 0.5670 (mmm) outliers start: 142 outliers final: 106 residues processed: 482 average time/residue: 0.3736 time to fit residues: 309.3894 Evaluate side-chains 464 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 345 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1335 HIS Chi-restraints excluded: chain A residue 1360 PHE Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1470 LYS Chi-restraints excluded: chain A residue 1495 TYR Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1531 PHE Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 SER Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1631 ILE Chi-restraints excluded: chain A residue 1659 LEU Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1717 LYS Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1736 ASN Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1803 ILE Chi-restraints excluded: chain A residue 1898 GLU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1954 LEU Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 1987 CYS Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2015 ASN Chi-restraints excluded: chain A residue 2037 ARG Chi-restraints excluded: chain A residue 2045 LEU Chi-restraints excluded: chain A residue 2068 ASP Chi-restraints excluded: chain A residue 2098 GLU Chi-restraints excluded: chain A residue 2103 ILE Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2150 LEU Chi-restraints excluded: chain A residue 2155 HIS Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2348 VAL Chi-restraints excluded: chain A residue 2393 LEU Chi-restraints excluded: chain A residue 2423 TYR Chi-restraints excluded: chain A residue 2430 MET Chi-restraints excluded: chain A residue 2440 TYR Chi-restraints excluded: chain A residue 2454 HIS Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2510 SER Chi-restraints excluded: chain A residue 2530 VAL Chi-restraints excluded: chain A residue 2548 HIS Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2681 THR Chi-restraints excluded: chain A residue 2704 SER Chi-restraints excluded: chain A residue 2779 SER Chi-restraints excluded: chain A residue 2788 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1456 LEU Chi-restraints excluded: chain B residue 1476 VAL Chi-restraints excluded: chain B residue 1534 SER Chi-restraints excluded: chain B residue 1545 TRP Chi-restraints excluded: chain B residue 1548 PHE Chi-restraints excluded: chain B residue 1599 LEU Chi-restraints excluded: chain B residue 1697 ILE Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1735 THR Chi-restraints excluded: chain B residue 1739 ARG Chi-restraints excluded: chain B residue 1766 TRP Chi-restraints excluded: chain B residue 1772 SER Chi-restraints excluded: chain B residue 1788 LEU Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1817 ASP Chi-restraints excluded: chain B residue 1826 THR Chi-restraints excluded: chain B residue 1848 LEU Chi-restraints excluded: chain B residue 1856 SER Chi-restraints excluded: chain B residue 1867 SER Chi-restraints excluded: chain B residue 1920 THR Chi-restraints excluded: chain B residue 1965 LEU Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 2011 LEU Chi-restraints excluded: chain B residue 2072 ARG Chi-restraints excluded: chain B residue 2089 SER Chi-restraints excluded: chain B residue 2109 SER Chi-restraints excluded: chain B residue 2136 GLU Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2150 LEU Chi-restraints excluded: chain B residue 2237 LEU Chi-restraints excluded: chain B residue 2241 THR Chi-restraints excluded: chain B residue 2301 ILE Chi-restraints excluded: chain B residue 2351 ILE Chi-restraints excluded: chain B residue 2367 LEU Chi-restraints excluded: chain B residue 2402 VAL Chi-restraints excluded: chain B residue 2403 ASP Chi-restraints excluded: chain B residue 2428 ILE Chi-restraints excluded: chain B residue 2446 VAL Chi-restraints excluded: chain B residue 2459 ILE Chi-restraints excluded: chain B residue 2465 ILE Chi-restraints excluded: chain B residue 2474 THR Chi-restraints excluded: chain B residue 2515 SER Chi-restraints excluded: chain B residue 2645 VAL Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2684 GLU Chi-restraints excluded: chain B residue 2711 VAL Chi-restraints excluded: chain B residue 2729 LYS Chi-restraints excluded: chain B residue 2781 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 179 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 429 optimal weight: 10.0000 chunk 293 optimal weight: 40.0000 chunk 254 optimal weight: 50.0000 chunk 168 optimal weight: 2.9990 chunk 427 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 29 optimal weight: 50.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2422 ASN ** B1394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2373 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.165662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.135527 restraints weight = 68360.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.134499 restraints weight = 49320.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.136033 restraints weight = 39322.797| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32456 Z= 0.175 Angle : 0.698 14.373 44416 Z= 0.355 Chirality : 0.042 0.236 5522 Planarity : 0.004 0.055 5830 Dihedral : 5.846 124.801 5061 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.48 % Favored : 93.44 % Rotamer: Outliers : 4.87 % Allowed : 35.22 % Favored : 59.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 4708 helix: 1.20 (0.10), residues: 3055 sheet: -2.09 (0.62), residues: 51 loop : -2.03 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B2275 HIS 0.009 0.001 HIS A2083 PHE 0.051 0.002 PHE A2229 TYR 0.032 0.002 TYR A1276 ARG 0.007 0.001 ARG B2359 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 2146) hydrogen bonds : angle 4.53549 ( 6363) SS BOND : bond 0.01147 ( 1) SS BOND : angle 1.54151 ( 2) covalent geometry : bond 0.00387 (32454) covalent geometry : angle 0.69776 (44414) Misc. bond : bond 0.00226 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 375 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1250 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7564 (t80) REVERT: A 1731 LEU cc_start: 0.5021 (OUTLIER) cc_final: 0.4754 (mm) REVERT: A 1987 CYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6403 (t) REVERT: A 2033 LEU cc_start: 0.6348 (tp) cc_final: 0.6058 (tt) REVERT: A 2037 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.5822 (tpm170) REVERT: A 2202 LEU cc_start: 0.7058 (pp) cc_final: 0.6418 (tp) REVERT: A 2476 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5328 (mtmm) REVERT: A 2710 GLU cc_start: 0.7885 (pt0) cc_final: 0.7172 (tt0) REVERT: A 2713 ARG cc_start: 0.7278 (mtm180) cc_final: 0.7002 (mtm-85) REVERT: B 1195 SER cc_start: 0.9078 (m) cc_final: 0.8791 (p) REVERT: B 1207 GLN cc_start: 0.8001 (mm110) cc_final: 0.7792 (pp30) REVERT: B 1239 VAL cc_start: 0.4974 (OUTLIER) cc_final: 0.4731 (p) REVERT: B 1543 MET cc_start: 0.7193 (mmt) cc_final: 0.6879 (mmt) REVERT: B 1766 TRP cc_start: 0.6266 (OUTLIER) cc_final: 0.5771 (t60) REVERT: B 2072 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6412 (mtm-85) REVERT: B 2107 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.7700 (m) REVERT: B 2239 MET cc_start: 0.6233 (ptp) cc_final: 0.6021 (ptp) REVERT: B 2275 TRP cc_start: 0.7694 (t60) cc_final: 0.7365 (t60) REVERT: B 2624 HIS cc_start: 0.6931 (t-170) cc_final: 0.6656 (t70) REVERT: B 2728 MET cc_start: 0.4152 (ttt) cc_final: 0.2413 (ptt) REVERT: B 2729 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.6597 (mttt) REVERT: B 2733 MET cc_start: 0.5616 (mmp) cc_final: 0.5233 (mmm) outliers start: 109 outliers final: 88 residues processed: 462 average time/residue: 0.3789 time to fit residues: 300.1827 Evaluate side-chains 455 residues out of total 4531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 357 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 1250 PHE Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1335 HIS Chi-restraints excluded: chain A residue 1360 PHE Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1470 LYS Chi-restraints excluded: chain A residue 1495 TYR Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1531 PHE Chi-restraints excluded: chain A residue 1558 HIS Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 SER Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1717 LYS Chi-restraints excluded: chain A residue 1722 VAL Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1898 GLU Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1954 LEU Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 1987 CYS Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2015 ASN Chi-restraints excluded: chain A residue 2037 ARG Chi-restraints excluded: chain A residue 2045 LEU Chi-restraints excluded: chain A residue 2098 GLU Chi-restraints excluded: chain A residue 2103 ILE Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2150 LEU Chi-restraints excluded: chain A residue 2155 HIS Chi-restraints excluded: chain A residue 2273 THR Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2348 VAL Chi-restraints excluded: chain A residue 2423 TYR Chi-restraints excluded: chain A residue 2454 HIS Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2474 THR Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2510 SER Chi-restraints excluded: chain A residue 2530 VAL Chi-restraints excluded: chain A residue 2548 HIS Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2681 THR Chi-restraints excluded: chain A residue 2704 SER Chi-restraints excluded: chain A residue 2788 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1268 ILE Chi-restraints excluded: chain B residue 1419 PHE Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1456 LEU Chi-restraints excluded: chain B residue 1534 SER Chi-restraints excluded: chain B residue 1545 TRP Chi-restraints excluded: chain B residue 1548 PHE Chi-restraints excluded: chain B residue 1599 LEU Chi-restraints excluded: chain B residue 1697 ILE Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1735 THR Chi-restraints excluded: chain B residue 1739 ARG Chi-restraints excluded: chain B residue 1766 TRP Chi-restraints excluded: chain B residue 1772 SER Chi-restraints excluded: chain B residue 1788 LEU Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1826 THR Chi-restraints excluded: chain B residue 1856 SER Chi-restraints excluded: chain B residue 1867 SER Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 2011 LEU Chi-restraints excluded: chain B residue 2072 ARG Chi-restraints excluded: chain B residue 2107 SER Chi-restraints excluded: chain B residue 2136 GLU Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2150 LEU Chi-restraints excluded: chain B residue 2241 THR Chi-restraints excluded: chain B residue 2301 ILE Chi-restraints excluded: chain B residue 2351 ILE Chi-restraints excluded: chain B residue 2370 LEU Chi-restraints excluded: chain B residue 2402 VAL Chi-restraints excluded: chain B residue 2403 ASP Chi-restraints excluded: chain B residue 2428 ILE Chi-restraints excluded: chain B residue 2459 ILE Chi-restraints excluded: chain B residue 2465 ILE Chi-restraints excluded: chain B residue 2474 THR Chi-restraints excluded: chain B residue 2515 SER Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2711 VAL Chi-restraints excluded: chain B residue 2729 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 409 optimal weight: 4.9990 chunk 78 optimal weight: 40.0000 chunk 400 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 345 optimal weight: 30.0000 chunk 353 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 398 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1959 ASN A2422 ASN ** B1394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2373 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.168674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.139141 restraints weight = 68970.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.137877 restraints weight = 48797.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.139438 restraints weight = 36664.755| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32456 Z= 0.128 Angle : 0.667 14.740 44416 Z= 0.333 Chirality : 0.040 0.236 5522 Planarity : 0.003 0.055 5830 Dihedral : 5.482 127.040 5059 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.99 % Favored : 93.90 % Rotamer: Outliers : 4.11 % Allowed : 36.29 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4708 helix: 1.47 (0.10), residues: 3069 sheet: -1.82 (0.67), residues: 52 loop : -1.99 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B2275 HIS 0.008 0.001 HIS A2339 PHE 0.050 0.002 PHE A2229 TYR 0.031 0.001 TYR A1276 ARG 0.009 0.000 ARG B2359 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 2146) hydrogen bonds : angle 4.28361 ( 6363) SS BOND : bond 0.00988 ( 1) SS BOND : angle 1.43052 ( 2) covalent geometry : bond 0.00274 (32454) covalent geometry : angle 0.66733 (44414) Misc. bond : bond 0.00177 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10720.64 seconds wall clock time: 190 minutes 0.97 seconds (11400.97 seconds total)