Starting phenix.real_space_refine on Tue Aug 26 20:55:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dnt_47058/08_2025/9dnt_47058.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dnt_47058/08_2025/9dnt_47058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dnt_47058/08_2025/9dnt_47058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dnt_47058/08_2025/9dnt_47058.map" model { file = "/net/cci-nas-00/data/ceres_data/9dnt_47058/08_2025/9dnt_47058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dnt_47058/08_2025/9dnt_47058.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 S 94 5.16 5 C 12981 2.51 5 N 3305 2.21 5 O 3703 1.98 5 H 20216 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40299 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 40299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2490, 40299 Classifications: {'peptide': 2490} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 94, 'TRANS': 2393} Chain breaks: 26 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 3, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 5.71, per 1000 atoms: 0.14 Number of scatterers: 40299 At special positions: 0 Unit cell: (144.42, 131.97, 159.36, 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 94 16.00 O 3703 8.00 N 3305 7.00 C 12981 6.00 H 20216 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4826 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 9 sheets defined 75.3% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.611A pdb=" N GLU A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 73 removed outlier: 3.517A pdb=" N ARG A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.798A pdb=" N MET A 100 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.845A pdb=" N VAL A 116 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.751A pdb=" N LEU A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 removed outlier: 3.510A pdb=" N LYS A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 152 Processing helix chain 'A' and resid 164 through 176 Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.535A pdb=" N TYR A 196 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.743A pdb=" N CYS A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 260 Processing helix chain 'A' and resid 263 through 281 removed outlier: 3.625A pdb=" N TRP A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASP A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 309 removed outlier: 4.101A pdb=" N ASP A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.516A pdb=" N LEU A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 358 removed outlier: 3.507A pdb=" N LEU A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS A 358 " --> pdb=" O CYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.883A pdb=" N CYS A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER A 363 " --> pdb=" O HIS A 359 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 392 Processing helix chain 'A' and resid 397 through 413 Processing helix chain 'A' and resid 414 through 425 Processing helix chain 'A' and resid 425 through 435 removed outlier: 3.759A pdb=" N THR A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 456 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 469 through 488 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 506 through 526 Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.553A pdb=" N ARG A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 549 through 571 removed outlier: 7.377A pdb=" N LEU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N THR A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 575 through 583 Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 599 through 615 Proline residue: A 607 - end of helix Processing helix chain 'A' and resid 616 through 627 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.583A pdb=" N ASN A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 633 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A 635 " --> pdb=" O ASN A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 648 through 665 Processing helix chain 'A' and resid 665 through 687 removed outlier: 3.927A pdb=" N LYS A 669 " --> pdb=" O TYR A 665 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A 670 " --> pdb=" O PRO A 666 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 684 - end of helix removed outlier: 3.734A pdb=" N PHE A 687 " --> pdb=" O MET A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 746 removed outlier: 3.625A pdb=" N SER A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 6.248A pdb=" N PHE A 750 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 removed outlier: 3.522A pdb=" N PHE A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 766 " --> pdb=" O PHE A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 777 Processing helix chain 'A' and resid 778 through 795 Processing helix chain 'A' and resid 799 through 814 Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 834 through 857 removed outlier: 3.509A pdb=" N SER A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 863 removed outlier: 3.611A pdb=" N LEU A 863 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 879 Processing helix chain 'A' and resid 880 through 902 removed outlier: 3.547A pdb=" N LYS A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 912 removed outlier: 3.614A pdb=" N THR A 910 " --> pdb=" O ASP A 906 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 911 " --> pdb=" O SER A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 975 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 984 through 1009 removed outlier: 3.755A pdb=" N THR A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR A1009 " --> pdb=" O MET A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1029 removed outlier: 3.748A pdb=" N VAL A1020 " --> pdb=" O PRO A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1053 Processing helix chain 'A' and resid 1054 through 1072 removed outlier: 3.543A pdb=" N LYS A1072 " --> pdb=" O THR A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1082 Processing helix chain 'A' and resid 1088 through 1107 Processing helix chain 'A' and resid 1109 through 1113 removed outlier: 3.698A pdb=" N MET A1113 " --> pdb=" O THR A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1122 Processing helix chain 'A' and resid 1131 through 1154 removed outlier: 3.627A pdb=" N THR A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A1138 " --> pdb=" O LYS A1134 " (cutoff:3.500A) Proline residue: A1139 - end of helix Processing helix chain 'A' and resid 1166 through 1181 Processing helix chain 'A' and resid 1202 through 1213 Processing helix chain 'A' and resid 1215 through 1226 Processing helix chain 'A' and resid 1233 through 1237 removed outlier: 4.407A pdb=" N ILE A1236 " --> pdb=" O ASP A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1251 removed outlier: 3.513A pdb=" N LYS A1249 " --> pdb=" O GLU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1259 removed outlier: 3.541A pdb=" N TYR A1258 " --> pdb=" O LYS A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1285 Processing helix chain 'A' and resid 1287 through 1296 removed outlier: 6.198A pdb=" N PHE A1293 " --> pdb=" O PRO A1289 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1301 Proline residue: A1300 - end of helix No H-bonds generated for 'chain 'A' and resid 1297 through 1301' Processing helix chain 'A' and resid 1302 through 1318 Processing helix chain 'A' and resid 1320 through 1335 removed outlier: 3.643A pdb=" N PHE A1324 " --> pdb=" O PRO A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1356 removed outlier: 3.611A pdb=" N SER A1345 " --> pdb=" O ALA A1341 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A1356 " --> pdb=" O ILE A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1363 Processing helix chain 'A' and resid 1363 through 1378 Processing helix chain 'A' and resid 1379 through 1383 Processing helix chain 'A' and resid 1385 through 1403 removed outlier: 4.159A pdb=" N SER A1389 " --> pdb=" O THR A1385 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A1390 " --> pdb=" O PRO A1386 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A1401 " --> pdb=" O ILE A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1443 Processing helix chain 'A' and resid 1449 through 1464 removed outlier: 3.619A pdb=" N PHE A1462 " --> pdb=" O ARG A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1477 Processing helix chain 'A' and resid 1477 through 1489 removed outlier: 3.523A pdb=" N ARG A1481 " --> pdb=" O GLY A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1511 removed outlier: 3.860A pdb=" N LEU A1498 " --> pdb=" O LYS A1494 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A1510 " --> pdb=" O THR A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1530 Processing helix chain 'A' and resid 1543 through 1550 Processing helix chain 'A' and resid 1550 through 1557 removed outlier: 3.572A pdb=" N SER A1557 " --> pdb=" O VAL A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1569 Processing helix chain 'A' and resid 1611 through 1626 removed outlier: 3.663A pdb=" N LYS A1626 " --> pdb=" O ALA A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1671 Processing helix chain 'A' and resid 1671 through 1680 Processing helix chain 'A' and resid 1695 through 1704 Processing helix chain 'A' and resid 1717 through 1738 Processing helix chain 'A' and resid 1754 through 1777 Processing helix chain 'A' and resid 1777 through 1785 removed outlier: 4.233A pdb=" N LEU A1781 " --> pdb=" O SER A1777 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1782 " --> pdb=" O SER A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1785 through 1802 removed outlier: 3.616A pdb=" N VAL A1800 " --> pdb=" O ILE A1796 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A1802 " --> pdb=" O SER A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1817 through 1831 Processing helix chain 'A' and resid 1831 through 1842 Processing helix chain 'A' and resid 1849 through 1868 removed outlier: 3.506A pdb=" N PHE A1854 " --> pdb=" O SER A1850 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN A1855 " --> pdb=" O LYS A1851 " (cutoff:3.500A) Processing helix chain 'A' and resid 2226 through 2239 removed outlier: 3.630A pdb=" N PHE A2238 " --> pdb=" O ILE A2234 " (cutoff:3.500A) Processing helix chain 'A' and resid 2243 through 2247 Processing helix chain 'A' and resid 2248 through 2264 removed outlier: 3.742A pdb=" N VAL A2252 " --> pdb=" O ILE A2248 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A2257 " --> pdb=" O ILE A2253 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS A2258 " --> pdb=" O ASN A2254 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A2259 " --> pdb=" O ARG A2255 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA A2262 " --> pdb=" O LYS A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2458 through 2465 removed outlier: 3.781A pdb=" N LYS A2465 " --> pdb=" O ALA A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2469 removed outlier: 3.669A pdb=" N ILE A2469 " --> pdb=" O SER A2466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2466 through 2469' Processing helix chain 'A' and resid 2477 through 2487 Processing helix chain 'A' and resid 2489 through 2507 Processing helix chain 'A' and resid 2510 through 2527 Processing helix chain 'A' and resid 2542 through 2561 Processing helix chain 'A' and resid 2562 through 2570 removed outlier: 4.298A pdb=" N TYR A2566 " --> pdb=" O SER A2562 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A2567 " --> pdb=" O ARG A2563 " (cutoff:3.500A) Processing helix chain 'A' and resid 2597 through 2605 removed outlier: 4.007A pdb=" N LEU A2601 " --> pdb=" O PRO A2597 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A2604 " --> pdb=" O HIS A2600 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A2605 " --> pdb=" O LEU A2601 " (cutoff:3.500A) Processing helix chain 'A' and resid 2607 through 2612 Processing helix chain 'A' and resid 2613 through 2637 Processing helix chain 'A' and resid 2654 through 2667 removed outlier: 3.897A pdb=" N ILE A2664 " --> pdb=" O LYS A2660 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A2665 " --> pdb=" O ILE A2661 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET A2666 " --> pdb=" O LEU A2662 " (cutoff:3.500A) Processing helix chain 'A' and resid 2671 through 2688 removed outlier: 3.725A pdb=" N LEU A2688 " --> pdb=" O ASN A2684 " (cutoff:3.500A) Processing helix chain 'A' and resid 2691 through 2724 removed outlier: 3.574A pdb=" N SER A2701 " --> pdb=" O LYS A2697 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A2708 " --> pdb=" O ILE A2704 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS A2709 " --> pdb=" O SER A2705 " (cutoff:3.500A) Processing helix chain 'A' and resid 2731 through 2740 removed outlier: 3.573A pdb=" N LYS A2737 " --> pdb=" O GLU A2733 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A2738 " --> pdb=" O LEU A2734 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A2740 " --> pdb=" O GLN A2736 " (cutoff:3.500A) Processing helix chain 'A' and resid 2743 through 2759 Processing helix chain 'A' and resid 2770 through 2780 Processing helix chain 'A' and resid 2782 through 2799 Processing helix chain 'A' and resid 2806 through 2808 No H-bonds generated for 'chain 'A' and resid 2806 through 2808' Processing helix chain 'A' and resid 2809 through 2819 Processing helix chain 'A' and resid 2851 through 2857 Processing helix chain 'A' and resid 2859 through 2870 removed outlier: 3.755A pdb=" N GLN A2865 " --> pdb=" O LYS A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2871 through 2884 Proline residue: A2877 - end of helix removed outlier: 3.692A pdb=" N LEU A2880 " --> pdb=" O PRO A2877 " (cutoff:3.500A) Processing helix chain 'A' and resid 2889 through 2902 Processing helix chain 'A' and resid 2919 through 2929 Processing helix chain 'A' and resid 2932 through 2939 Processing helix chain 'A' and resid 2957 through 2969 removed outlier: 3.722A pdb=" N PHE A2969 " --> pdb=" O SER A2965 " (cutoff:3.500A) Processing helix chain 'A' and resid 2970 through 2974 Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3024 through 3032 Processing helix chain 'A' and resid 3037 through 3044 Processing helix chain 'A' and resid 3046 through 3056 removed outlier: 3.646A pdb=" N VAL A3053 " --> pdb=" O TYR A3049 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP A3054 " --> pdb=" O LYS A3050 " (cutoff:3.500A) Processing helix chain 'A' and resid 3093 through 3096 Processing helix chain 'A' and resid 3097 through 3110 removed outlier: 3.790A pdb=" N LYS A3102 " --> pdb=" O GLN A3098 " (cutoff:3.500A) Processing helix chain 'A' and resid 3113 through 3126 Processing helix chain 'A' and resid 3129 through 3134 Processing helix chain 'A' and resid 3137 through 3146 removed outlier: 3.731A pdb=" N GLU A3142 " --> pdb=" O GLU A3138 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A3143 " --> pdb=" O GLN A3139 " (cutoff:3.500A) Processing helix chain 'A' and resid 3155 through 3159 Processing helix chain 'A' and resid 3169 through 3182 Processing helix chain 'A' and resid 3183 through 3196 Processing helix chain 'A' and resid 3204 through 3208 Processing helix chain 'A' and resid 3246 through 3261 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.629A pdb=" N ASP A 49 " --> pdb=" O GLU A 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 1030 through 1031 Processing sheet with id=AA5, first strand: chain 'A' and resid 1541 through 1542 removed outlier: 3.512A pdb=" N ARG A1541 " --> pdb=" O LEU A1585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2911 through 2915 removed outlier: 3.500A pdb=" N GLU A2942 " --> pdb=" O LEU A2911 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2976 through 2979 removed outlier: 5.825A pdb=" N THR A2985 " --> pdb=" O VAL A2979 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3069 through 3074 Processing sheet with id=AA9, first strand: chain 'A' and resid 3160 through 3163 removed outlier: 6.448A pdb=" N THR A3161 " --> pdb=" O ILE A3219 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ARG A3221 " --> pdb=" O THR A3161 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL A3163 " --> pdb=" O ARG A3221 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER A3218 " --> pdb=" O LEU A3239 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU A3241 " --> pdb=" O SER A3218 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N HIS A3220 " --> pdb=" O LEU A3241 " (cutoff:3.500A) 1221 hydrogen bonds defined for protein. 3528 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: 10.31 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20183 1.03 - 1.23: 265 1.23 - 1.43: 8167 1.43 - 1.62: 11923 1.62 - 1.82: 154 Bond restraints: 40692 Sorted by residual: bond pdb=" CA ILE A 41 " pdb=" CB ILE A 41 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.22e-01 bond pdb=" N PRO A 598 " pdb=" CA PRO A 598 " ideal model delta sigma weight residual 1.469 1.478 -0.010 1.28e-02 6.10e+03 5.64e-01 bond pdb=" CG MET A 183 " pdb=" SD MET A 183 " ideal model delta sigma weight residual 1.803 1.820 -0.017 2.50e-02 1.60e+03 4.51e-01 bond pdb=" C LEU A1288 " pdb=" N PRO A1289 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 4.29e-01 bond pdb=" CB GLN A 891 " pdb=" CG GLN A 891 " ideal model delta sigma weight residual 1.520 1.501 0.019 3.00e-02 1.11e+03 4.14e-01 ... (remaining 40687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.01: 73674 6.01 - 12.02: 3 12.02 - 18.04: 0 18.04 - 24.05: 2 24.05 - 30.06: 4 Bond angle restraints: 73683 Sorted by residual: angle pdb="HD21 LEU A2975 " pdb=" CD2 LEU A2975 " pdb="HD23 LEU A2975 " ideal model delta sigma weight residual 110.00 79.94 30.06 3.00e+00 1.11e-01 1.00e+02 angle pdb="HD21 LEU A2975 " pdb=" CD2 LEU A2975 " pdb="HD22 LEU A2975 " ideal model delta sigma weight residual 110.00 80.29 29.71 3.00e+00 1.11e-01 9.81e+01 angle pdb=" CG LEU A2975 " pdb=" CD2 LEU A2975 " pdb="HD23 LEU A2975 " ideal model delta sigma weight residual 109.00 80.23 28.77 3.00e+00 1.11e-01 9.20e+01 angle pdb=" CG LEU A2975 " pdb=" CD2 LEU A2975 " pdb="HD22 LEU A2975 " ideal model delta sigma weight residual 109.00 80.98 28.02 3.00e+00 1.11e-01 8.72e+01 angle pdb=" CG LEU A2975 " pdb=" CD2 LEU A2975 " pdb="HD21 LEU A2975 " ideal model delta sigma weight residual 109.00 131.44 -22.44 3.00e+00 1.11e-01 5.59e+01 ... (remaining 73678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 17352 17.81 - 35.62: 1354 35.62 - 53.44: 298 53.44 - 71.25: 58 71.25 - 89.06: 21 Dihedral angle restraints: 19083 sinusoidal: 10352 harmonic: 8731 Sorted by residual: dihedral pdb=" CA THR A1867 " pdb=" C THR A1867 " pdb=" N ARG A1868 " pdb=" CA ARG A1868 " ideal model delta harmonic sigma weight residual 180.00 163.11 16.89 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLN A1043 " pdb=" C GLN A1043 " pdb=" N THR A1044 " pdb=" CA THR A1044 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP A1075 " pdb=" CB ASP A1075 " pdb=" CG ASP A1075 " pdb=" OD1 ASP A1075 " ideal model delta sinusoidal sigma weight residual -30.00 -85.94 55.94 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 19080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2136 0.027 - 0.053: 685 0.053 - 0.080: 269 0.080 - 0.107: 93 0.107 - 0.133: 32 Chirality restraints: 3215 Sorted by residual: chirality pdb=" CA ILE A2913 " pdb=" N ILE A2913 " pdb=" C ILE A2913 " pdb=" CB ILE A2913 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A3081 " pdb=" N ILE A3081 " pdb=" C ILE A3081 " pdb=" CB ILE A3081 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL A3200 " pdb=" N VAL A3200 " pdb=" C VAL A3200 " pdb=" CB VAL A3200 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 3212 not shown) Planarity restraints: 5817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1200 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A1201 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A1201 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1201 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A3241 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO A3242 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A3242 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A3242 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 427 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 428 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " 0.018 5.00e-02 4.00e+02 ... (remaining 5814 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1776 2.18 - 2.78: 82386 2.78 - 3.39: 117475 3.39 - 3.99: 147384 3.99 - 4.60: 234319 Nonbonded interactions: 583340 Sorted by model distance: nonbonded pdb=" H SER A 250 " pdb=" OE1 GLN A 253 " model vdw 1.572 2.450 nonbonded pdb=" O GLY A3086 " pdb=" H ILE A3090 " model vdw 1.591 2.450 nonbonded pdb=" O PHE A 304 " pdb=" HG1 THR A 307 " model vdw 1.603 2.450 nonbonded pdb=" O LEU A 107 " pdb=" HG1 THR A 111 " model vdw 1.606 2.450 nonbonded pdb=" HG1 THR A1044 " pdb=" O GLU A1114 " model vdw 1.612 2.450 ... (remaining 583335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.240 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 33.220 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20476 Z= 0.136 Angle : 0.434 6.791 27680 Z= 0.230 Chirality : 0.034 0.133 3215 Planarity : 0.003 0.036 3461 Dihedral : 14.566 89.059 7631 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.89 % Allowed : 10.91 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.18), residues: 2436 helix: 1.96 (0.13), residues: 1634 sheet: -0.36 (0.72), residues: 56 loop : 0.25 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1704 TYR 0.011 0.001 TYR A 96 PHE 0.010 0.001 PHE A 506 TRP 0.008 0.001 TRP A3156 HIS 0.002 0.000 HIS A 840 Details of bonding type rmsd covalent geometry : bond 0.00297 (20476) covalent geometry : angle 0.43435 (27680) hydrogen bonds : bond 0.14391 ( 1221) hydrogen bonds : angle 5.84295 ( 3528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue THR 1160 is missing expected H atoms. Skipping. Residue LEU 1410 is missing expected H atoms. Skipping. Residue SER 1411 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue THR 1686 is missing expected H atoms. Skipping. Residue TYR 1687 is missing expected H atoms. Skipping. Residue ALA 1688 is missing expected H atoms. Skipping. Residue LEU 1845 is missing expected H atoms. Skipping. Residue VAL 2259 is missing expected H atoms. Skipping. Residue SER 2260 is missing expected H atoms. Skipping. Residue LEU 2261 is missing expected H atoms. Skipping. Residue LEU 2263 is missing expected H atoms. Skipping. Residue LEU 2901 is missing expected H atoms. Skipping. Residue SER 3043 is missing expected H atoms. Skipping. Residue LEU 3044 is missing expected H atoms. Skipping. Residue TYR 3048 is missing expected H atoms. Skipping. Residue TYR 3049 is missing expected H atoms. Skipping. Residue LEU 3052 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue ILE 3055 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1000 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8480 (OUTLIER) REVERT: A 1067 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: A 2223 ILE cc_start: 0.9246 (tp) cc_final: 0.8937 (pp) REVERT: A 2526 MET cc_start: 0.7673 (mtp) cc_final: 0.7302 (tmm) REVERT: A 2919 GLN cc_start: 0.8652 (mp10) cc_final: 0.8126 (tt0) REVERT: A 2960 TRP cc_start: 0.8268 (t60) cc_final: 0.7775 (t60) outliers start: 20 outliers final: 11 residues processed: 92 average time/residue: 1.0441 time to fit residues: 111.3646 Evaluate side-chains 84 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1000 GLU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 2901 LEU Chi-restraints excluded: chain A residue 2977 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3235 CYS Chi-restraints excluded: chain A residue 3236 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A3203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.063375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.044049 restraints weight = 251333.073| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.80 r_work: 0.2880 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20476 Z= 0.215 Angle : 0.503 6.151 27680 Z= 0.274 Chirality : 0.036 0.141 3215 Planarity : 0.004 0.036 3461 Dihedral : 4.719 59.876 2700 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.29 % Allowed : 11.18 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.18), residues: 2436 helix: 2.04 (0.13), residues: 1664 sheet: -0.37 (0.81), residues: 45 loop : 0.06 (0.25), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 11 TYR 0.013 0.001 TYR A3107 PHE 0.013 0.001 PHE A 270 TRP 0.008 0.001 TRP A3156 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00462 (20476) covalent geometry : angle 0.50274 (27680) hydrogen bonds : bond 0.04926 ( 1221) hydrogen bonds : angle 4.62896 ( 3528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue THR 1160 is missing expected H atoms. Skipping. Residue LEU 1410 is missing expected H atoms. Skipping. Residue SER 1411 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue THR 1686 is missing expected H atoms. Skipping. Residue TYR 1687 is missing expected H atoms. Skipping. Residue ALA 1688 is missing expected H atoms. Skipping. Residue LEU 1845 is missing expected H atoms. Skipping. Residue VAL 2259 is missing expected H atoms. Skipping. Residue SER 2260 is missing expected H atoms. Skipping. Residue LEU 2261 is missing expected H atoms. Skipping. Residue LEU 2263 is missing expected H atoms. Skipping. Residue LEU 2901 is missing expected H atoms. Skipping. Residue SER 3043 is missing expected H atoms. Skipping. Residue LEU 3044 is missing expected H atoms. Skipping. Residue TYR 3048 is missing expected H atoms. Skipping. Residue TYR 3049 is missing expected H atoms. Skipping. Residue LEU 3052 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue ILE 3055 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1000 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8469 (OUTLIER) REVERT: A 1067 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: A 2526 MET cc_start: 0.7806 (mtp) cc_final: 0.7351 (tmm) REVERT: A 3156 TRP cc_start: 0.8854 (t-100) cc_final: 0.7904 (t-100) outliers start: 29 outliers final: 14 residues processed: 93 average time/residue: 0.9036 time to fit residues: 99.6960 Evaluate side-chains 84 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1000 GLU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2850 ASN Chi-restraints excluded: chain A residue 2901 LEU Chi-restraints excluded: chain A residue 2977 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3236 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 147 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 196 optimal weight: 0.3980 chunk 193 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.063428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.044241 restraints weight = 249905.052| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.76 r_work: 0.2887 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20476 Z= 0.172 Angle : 0.473 6.027 27680 Z= 0.253 Chirality : 0.036 0.149 3215 Planarity : 0.003 0.037 3461 Dihedral : 4.398 59.962 2692 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.20 % Allowed : 11.80 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.18), residues: 2436 helix: 2.10 (0.13), residues: 1667 sheet: -0.51 (0.83), residues: 45 loop : -0.01 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 681 TYR 0.014 0.001 TYR A 96 PHE 0.014 0.001 PHE A 270 TRP 0.006 0.001 TRP A 267 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00378 (20476) covalent geometry : angle 0.47314 (27680) hydrogen bonds : bond 0.04169 ( 1221) hydrogen bonds : angle 4.32042 ( 3528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue THR 1160 is missing expected H atoms. Skipping. Residue LEU 1410 is missing expected H atoms. Skipping. Residue SER 1411 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue THR 1686 is missing expected H atoms. Skipping. Residue TYR 1687 is missing expected H atoms. Skipping. Residue ALA 1688 is missing expected H atoms. Skipping. Residue LEU 1845 is missing expected H atoms. Skipping. Residue VAL 2259 is missing expected H atoms. Skipping. Residue SER 2260 is missing expected H atoms. Skipping. Residue LEU 2261 is missing expected H atoms. Skipping. Residue LEU 2263 is missing expected H atoms. Skipping. Residue LEU 2901 is missing expected H atoms. Skipping. Residue SER 3043 is missing expected H atoms. Skipping. Residue LEU 3044 is missing expected H atoms. Skipping. Residue TYR 3048 is missing expected H atoms. Skipping. Residue TYR 3049 is missing expected H atoms. Skipping. Residue LEU 3052 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue ILE 3055 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.799 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 1000 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8460 (OUTLIER) REVERT: A 1067 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8596 (m-80) REVERT: A 2526 MET cc_start: 0.7739 (mtp) cc_final: 0.7343 (tmm) REVERT: A 3107 TYR cc_start: 0.8700 (t80) cc_final: 0.8254 (t80) outliers start: 27 outliers final: 16 residues processed: 94 average time/residue: 0.9373 time to fit residues: 104.2693 Evaluate side-chains 87 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 897 GLU Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1000 GLU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2792 CYS Chi-restraints excluded: chain A residue 2850 ASN Chi-restraints excluded: chain A residue 2901 LEU Chi-restraints excluded: chain A residue 2977 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3235 CYS Chi-restraints excluded: chain A residue 3236 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 214 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** A2781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.063052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.043833 restraints weight = 250956.404| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.75 r_work: 0.2870 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20476 Z= 0.220 Angle : 0.489 6.099 27680 Z= 0.263 Chirality : 0.036 0.149 3215 Planarity : 0.003 0.038 3461 Dihedral : 4.445 59.910 2692 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.33 % Allowed : 11.88 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.18), residues: 2436 helix: 2.10 (0.13), residues: 1667 sheet: -0.52 (0.82), residues: 45 loop : -0.10 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 681 TYR 0.016 0.001 TYR A 96 PHE 0.013 0.001 PHE A 268 TRP 0.006 0.001 TRP A2599 HIS 0.003 0.001 HIS A 840 Details of bonding type rmsd covalent geometry : bond 0.00484 (20476) covalent geometry : angle 0.48910 (27680) hydrogen bonds : bond 0.03999 ( 1221) hydrogen bonds : angle 4.31038 ( 3528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue THR 1160 is missing expected H atoms. Skipping. Residue LEU 1410 is missing expected H atoms. Skipping. Residue SER 1411 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue THR 1686 is missing expected H atoms. Skipping. Residue TYR 1687 is missing expected H atoms. Skipping. Residue ALA 1688 is missing expected H atoms. Skipping. Residue LEU 1845 is missing expected H atoms. Skipping. Residue VAL 2259 is missing expected H atoms. Skipping. Residue SER 2260 is missing expected H atoms. Skipping. Residue LEU 2261 is missing expected H atoms. Skipping. Residue LEU 2263 is missing expected H atoms. Skipping. Residue LEU 2901 is missing expected H atoms. Skipping. Residue SER 3043 is missing expected H atoms. Skipping. Residue LEU 3044 is missing expected H atoms. Skipping. Residue TYR 3048 is missing expected H atoms. Skipping. Residue TYR 3049 is missing expected H atoms. Skipping. Residue LEU 3052 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue ILE 3055 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.769 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: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8590 (mtt) cc_final: 0.8361 (ttm) REVERT: A 1000 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8506 (OUTLIER) REVERT: A 1067 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: A 2526 MET cc_start: 0.7689 (mtp) cc_final: 0.7343 (tmm) outliers start: 30 outliers final: 22 residues processed: 99 average time/residue: 0.8997 time to fit residues: 105.9012 Evaluate side-chains 93 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 897 GLU Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1000 GLU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1358 TYR Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2792 CYS Chi-restraints excluded: chain A residue 2850 ASN Chi-restraints excluded: chain A residue 2901 LEU Chi-restraints excluded: chain A residue 2977 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3235 CYS Chi-restraints excluded: chain A residue 3236 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 117 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.063710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.044457 restraints weight = 249156.454| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.77 r_work: 0.2888 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20476 Z= 0.129 Angle : 0.450 6.447 27680 Z= 0.237 Chirality : 0.035 0.156 3215 Planarity : 0.003 0.041 3461 Dihedral : 4.393 59.930 2692 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.06 % Allowed : 12.51 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.18), residues: 2436 helix: 2.30 (0.13), residues: 1663 sheet: -0.43 (0.84), residues: 45 loop : -0.07 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 681 TYR 0.014 0.001 TYR A3107 PHE 0.012 0.001 PHE A 270 TRP 0.006 0.001 TRP A2599 HIS 0.003 0.001 HIS A1552 Details of bonding type rmsd covalent geometry : bond 0.00287 (20476) covalent geometry : angle 0.45009 (27680) hydrogen bonds : bond 0.03673 ( 1221) hydrogen bonds : angle 4.04433 ( 3528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue THR 1160 is missing expected H atoms. Skipping. Residue LEU 1410 is missing expected H atoms. Skipping. Residue SER 1411 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue THR 1686 is missing expected H atoms. Skipping. Residue TYR 1687 is missing expected H atoms. Skipping. Residue ALA 1688 is missing expected H atoms. Skipping. Residue LEU 1845 is missing expected H atoms. Skipping. Residue VAL 2259 is missing expected H atoms. Skipping. Residue SER 2260 is missing expected H atoms. Skipping. Residue LEU 2261 is missing expected H atoms. Skipping. Residue LEU 2263 is missing expected H atoms. Skipping. Residue LEU 2901 is missing expected H atoms. Skipping. Residue SER 3043 is missing expected H atoms. Skipping. Residue LEU 3044 is missing expected H atoms. Skipping. Residue TYR 3048 is missing expected H atoms. Skipping. Residue TYR 3049 is missing expected H atoms. Skipping. Residue LEU 3052 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue ILE 3055 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 1.059 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: symmetry clash revert: symmetry clash REVERT: A 1000 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8539 (OUTLIER) REVERT: A 1067 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8544 (m-80) REVERT: A 2526 MET cc_start: 0.7663 (mtp) cc_final: 0.7328 (tmm) REVERT: A 3107 TYR cc_start: 0.8737 (t80) cc_final: 0.8310 (t80) outliers start: 24 outliers final: 17 residues processed: 93 average time/residue: 0.9396 time to fit residues: 104.0001 Evaluate side-chains 88 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1000 GLU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1358 TYR Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2792 CYS Chi-restraints excluded: chain A residue 2850 ASN Chi-restraints excluded: chain A residue 2901 LEU Chi-restraints excluded: chain A residue 2977 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3236 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 39 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 135 optimal weight: 0.0070 chunk 204 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.063599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.044293 restraints weight = 249969.153| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.78 r_work: 0.2889 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20476 Z= 0.156 Angle : 0.457 7.512 27680 Z= 0.241 Chirality : 0.035 0.152 3215 Planarity : 0.003 0.040 3461 Dihedral : 4.379 59.862 2692 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.06 % Allowed : 12.77 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.18), residues: 2436 helix: 2.31 (0.13), residues: 1660 sheet: -0.36 (0.84), residues: 45 loop : -0.09 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 681 TYR 0.014 0.001 TYR A 96 PHE 0.013 0.001 PHE A2921 TRP 0.006 0.001 TRP A2599 HIS 0.002 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00344 (20476) covalent geometry : angle 0.45715 (27680) hydrogen bonds : bond 0.03635 ( 1221) hydrogen bonds : angle 4.03407 ( 3528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue THR 1160 is missing expected H atoms. Skipping. Residue LEU 1410 is missing expected H atoms. Skipping. Residue SER 1411 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue THR 1686 is missing expected H atoms. Skipping. Residue TYR 1687 is missing expected H atoms. Skipping. Residue ALA 1688 is missing expected H atoms. Skipping. Residue LEU 1845 is missing expected H atoms. Skipping. Residue VAL 2259 is missing expected H atoms. Skipping. Residue SER 2260 is missing expected H atoms. Skipping. Residue LEU 2261 is missing expected H atoms. Skipping. Residue LEU 2263 is missing expected H atoms. Skipping. Residue LEU 2901 is missing expected H atoms. Skipping. Residue SER 3043 is missing expected H atoms. Skipping. Residue LEU 3044 is missing expected H atoms. Skipping. Residue TYR 3048 is missing expected H atoms. Skipping. Residue TYR 3049 is missing expected H atoms. Skipping. Residue LEU 3052 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue ILE 3055 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.994 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: symmetry clash REVERT: A 453 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8542 (tm-30) REVERT: A 1000 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8511 (OUTLIER) REVERT: A 1067 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: A 2526 MET cc_start: 0.7614 (mtp) cc_final: 0.7305 (tmm) REVERT: A 3107 TYR cc_start: 0.8669 (t80) cc_final: 0.8246 (t80) outliers start: 24 outliers final: 19 residues processed: 92 average time/residue: 0.9668 time to fit residues: 104.9556 Evaluate side-chains 91 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1000 GLU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1358 TYR Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2792 CYS Chi-restraints excluded: chain A residue 2850 ASN Chi-restraints excluded: chain A residue 2901 LEU Chi-restraints excluded: chain A residue 2977 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3235 CYS Chi-restraints excluded: chain A residue 3236 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 98 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 239 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.063712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.044495 restraints weight = 251247.866| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.71 r_work: 0.2875 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20476 Z= 0.152 Angle : 0.458 8.928 27680 Z= 0.240 Chirality : 0.035 0.153 3215 Planarity : 0.003 0.041 3461 Dihedral : 4.365 59.733 2692 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.06 % Allowed : 12.95 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.18), residues: 2436 helix: 2.35 (0.13), residues: 1660 sheet: -0.33 (0.84), residues: 45 loop : -0.07 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 681 TYR 0.014 0.001 TYR A 96 PHE 0.012 0.001 PHE A2969 TRP 0.006 0.001 TRP A2599 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00336 (20476) covalent geometry : angle 0.45783 (27680) hydrogen bonds : bond 0.03568 ( 1221) hydrogen bonds : angle 3.97629 ( 3528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue THR 1160 is missing expected H atoms. Skipping. Residue LEU 1410 is missing expected H atoms. Skipping. Residue SER 1411 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue THR 1686 is missing expected H atoms. Skipping. Residue TYR 1687 is missing expected H atoms. Skipping. Residue ALA 1688 is missing expected H atoms. Skipping. Residue LEU 1845 is missing expected H atoms. Skipping. Residue VAL 2259 is missing expected H atoms. Skipping. Residue SER 2260 is missing expected H atoms. Skipping. Residue LEU 2261 is missing expected H atoms. Skipping. Residue LEU 2263 is missing expected H atoms. Skipping. Residue LEU 2901 is missing expected H atoms. Skipping. Residue SER 3043 is missing expected H atoms. Skipping. Residue LEU 3044 is missing expected H atoms. Skipping. Residue TYR 3048 is missing expected H atoms. Skipping. Residue TYR 3049 is missing expected H atoms. Skipping. Residue LEU 3052 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue ILE 3055 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.798 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 453 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8553 (tm-30) REVERT: A 1000 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8576 (OUTLIER) REVERT: A 1067 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: A 2526 MET cc_start: 0.7596 (mtp) cc_final: 0.7315 (tmm) REVERT: A 3107 TYR cc_start: 0.8666 (t80) cc_final: 0.8243 (t80) outliers start: 24 outliers final: 20 residues processed: 91 average time/residue: 0.9725 time to fit residues: 104.9645 Evaluate side-chains 91 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1000 GLU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1358 TYR Chi-restraints excluded: chain A residue 1613 MET Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2792 CYS Chi-restraints excluded: chain A residue 2850 ASN Chi-restraints excluded: chain A residue 2901 LEU Chi-restraints excluded: chain A residue 2977 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3235 CYS Chi-restraints excluded: chain A residue 3236 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2781 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.063807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.044613 restraints weight = 251559.157| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.71 r_work: 0.2878 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20476 Z= 0.141 Angle : 0.456 9.928 27680 Z= 0.237 Chirality : 0.035 0.154 3215 Planarity : 0.003 0.041 3461 Dihedral : 4.335 59.666 2692 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.11 % Allowed : 13.22 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.18), residues: 2436 helix: 2.41 (0.13), residues: 1660 sheet: -0.35 (0.84), residues: 45 loop : -0.03 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 681 TYR 0.013 0.001 TYR A 96 PHE 0.012 0.001 PHE A 270 TRP 0.006 0.001 TRP A2599 HIS 0.002 0.001 HIS A1406 Details of bonding type rmsd covalent geometry : bond 0.00313 (20476) covalent geometry : angle 0.45556 (27680) hydrogen bonds : bond 0.03490 ( 1221) hydrogen bonds : angle 3.91576 ( 3528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue THR 1160 is missing expected H atoms. Skipping. Residue LEU 1410 is missing expected H atoms. Skipping. Residue SER 1411 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue THR 1686 is missing expected H atoms. Skipping. Residue TYR 1687 is missing expected H atoms. Skipping. Residue ALA 1688 is missing expected H atoms. Skipping. Residue LEU 1845 is missing expected H atoms. Skipping. Residue VAL 2259 is missing expected H atoms. Skipping. Residue SER 2260 is missing expected H atoms. Skipping. Residue LEU 2261 is missing expected H atoms. Skipping. Residue LEU 2263 is missing expected H atoms. Skipping. Residue LEU 2901 is missing expected H atoms. Skipping. Residue SER 3043 is missing expected H atoms. Skipping. Residue LEU 3044 is missing expected H atoms. Skipping. Residue TYR 3048 is missing expected H atoms. Skipping. Residue TYR 3049 is missing expected H atoms. Skipping. Residue LEU 3052 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue ILE 3055 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 1.065 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 453 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8552 (tm-30) REVERT: A 1000 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8549 (OUTLIER) REVERT: A 1067 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8558 (m-80) REVERT: A 2526 MET cc_start: 0.7623 (mtp) cc_final: 0.7328 (tmm) REVERT: A 3107 TYR cc_start: 0.8653 (t80) cc_final: 0.8255 (t80) outliers start: 25 outliers final: 19 residues processed: 91 average time/residue: 0.9610 time to fit residues: 103.1810 Evaluate side-chains 89 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1000 GLU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1358 TYR Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2792 CYS Chi-restraints excluded: chain A residue 2850 ASN Chi-restraints excluded: chain A residue 2901 LEU Chi-restraints excluded: chain A residue 2977 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3235 CYS Chi-restraints excluded: chain A residue 3236 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 78 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 233 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.063790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.044630 restraints weight = 251756.331| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.72 r_work: 0.2890 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20476 Z= 0.148 Angle : 0.457 10.045 27680 Z= 0.239 Chirality : 0.035 0.153 3215 Planarity : 0.003 0.041 3461 Dihedral : 4.320 59.591 2692 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.06 % Allowed : 13.17 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.18), residues: 2436 helix: 2.42 (0.13), residues: 1660 sheet: -0.37 (0.84), residues: 45 loop : -0.01 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 681 TYR 0.013 0.001 TYR A 96 PHE 0.012 0.001 PHE A 270 TRP 0.007 0.001 TRP A2599 HIS 0.002 0.001 HIS A1406 Details of bonding type rmsd covalent geometry : bond 0.00328 (20476) covalent geometry : angle 0.45750 (27680) hydrogen bonds : bond 0.03470 ( 1221) hydrogen bonds : angle 3.90828 ( 3528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue THR 1160 is missing expected H atoms. Skipping. Residue LEU 1410 is missing expected H atoms. Skipping. Residue SER 1411 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue THR 1686 is missing expected H atoms. Skipping. Residue TYR 1687 is missing expected H atoms. Skipping. Residue ALA 1688 is missing expected H atoms. Skipping. Residue LEU 1845 is missing expected H atoms. Skipping. Residue VAL 2259 is missing expected H atoms. Skipping. Residue SER 2260 is missing expected H atoms. Skipping. Residue LEU 2261 is missing expected H atoms. Skipping. Residue LEU 2263 is missing expected H atoms. Skipping. Residue LEU 2901 is missing expected H atoms. Skipping. Residue SER 3043 is missing expected H atoms. Skipping. Residue LEU 3044 is missing expected H atoms. Skipping. Residue TYR 3048 is missing expected H atoms. Skipping. Residue TYR 3049 is missing expected H atoms. Skipping. Residue LEU 3052 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue ILE 3055 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8539 (tm-30) REVERT: A 1000 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8538 (tp30) REVERT: A 1067 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8560 (m-80) REVERT: A 2526 MET cc_start: 0.7625 (mtp) cc_final: 0.7330 (tmm) outliers start: 24 outliers final: 16 residues processed: 90 average time/residue: 0.9613 time to fit residues: 102.9084 Evaluate side-chains 87 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1000 GLU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1358 TYR Chi-restraints excluded: chain A residue 2792 CYS Chi-restraints excluded: chain A residue 2850 ASN Chi-restraints excluded: chain A residue 2901 LEU Chi-restraints excluded: chain A residue 2977 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3235 CYS Chi-restraints excluded: chain A residue 3236 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 203 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.064362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.045191 restraints weight = 248231.186| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.69 r_work: 0.2911 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20476 Z= 0.097 Angle : 0.454 10.723 27680 Z= 0.231 Chirality : 0.034 0.157 3215 Planarity : 0.003 0.042 3461 Dihedral : 4.267 59.426 2692 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.84 % Allowed : 13.53 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.18), residues: 2436 helix: 2.52 (0.13), residues: 1661 sheet: -0.35 (0.84), residues: 45 loop : 0.06 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 681 TYR 0.017 0.001 TYR A3107 PHE 0.012 0.001 PHE A 270 TRP 0.008 0.001 TRP A2599 HIS 0.003 0.000 HIS A1552 Details of bonding type rmsd covalent geometry : bond 0.00215 (20476) covalent geometry : angle 0.45430 (27680) hydrogen bonds : bond 0.03310 ( 1221) hydrogen bonds : angle 3.77485 ( 3528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 524 is missing expected H atoms. Skipping. Residue ILE 535 is missing expected H atoms. Skipping. Residue THR 1160 is missing expected H atoms. Skipping. Residue LEU 1410 is missing expected H atoms. Skipping. Residue SER 1411 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue THR 1686 is missing expected H atoms. Skipping. Residue TYR 1687 is missing expected H atoms. Skipping. Residue ALA 1688 is missing expected H atoms. Skipping. Residue LEU 1845 is missing expected H atoms. Skipping. Residue VAL 2259 is missing expected H atoms. Skipping. Residue SER 2260 is missing expected H atoms. Skipping. Residue LEU 2261 is missing expected H atoms. Skipping. Residue LEU 2263 is missing expected H atoms. Skipping. Residue LEU 2901 is missing expected H atoms. Skipping. Residue SER 3043 is missing expected H atoms. Skipping. Residue LEU 3044 is missing expected H atoms. Skipping. Residue TYR 3048 is missing expected H atoms. Skipping. Residue TYR 3049 is missing expected H atoms. Skipping. Residue LEU 3052 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue ILE 3055 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8494 (tm-30) REVERT: A 1000 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8510 (tp30) REVERT: A 1067 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8540 (m-80) REVERT: A 2526 MET cc_start: 0.7579 (mtp) cc_final: 0.7306 (tmm) REVERT: A 3007 MET cc_start: 0.8101 (tpp) cc_final: 0.7751 (mtt) outliers start: 19 outliers final: 14 residues processed: 87 average time/residue: 0.9635 time to fit residues: 100.2500 Evaluate side-chains 85 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 1000 GLU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1358 TYR Chi-restraints excluded: chain A residue 2792 CYS Chi-restraints excluded: chain A residue 2850 ASN Chi-restraints excluded: chain A residue 2901 LEU Chi-restraints excluded: chain A residue 2977 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3235 CYS Chi-restraints excluded: chain A residue 3236 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 239 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.063867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.044675 restraints weight = 251961.680| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.74 r_work: 0.2886 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20476 Z= 0.157 Angle : 0.467 10.570 27680 Z= 0.241 Chirality : 0.035 0.153 3215 Planarity : 0.003 0.041 3461 Dihedral : 4.159 59.406 2690 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.75 % Allowed : 13.57 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.18), residues: 2436 helix: 2.49 (0.13), residues: 1660 sheet: -0.40 (0.83), residues: 45 loop : 0.03 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 681 TYR 0.013 0.001 TYR A 96 PHE 0.012 0.001 PHE A 270 TRP 0.006 0.001 TRP A2599 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00348 (20476) covalent geometry : angle 0.46691 (27680) hydrogen bonds : bond 0.03404 ( 1221) hydrogen bonds : angle 3.85833 ( 3528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8229.97 seconds wall clock time: 140 minutes 19.45 seconds (8419.45 seconds total)