Starting phenix.real_space_refine on Fri Mar 6 02:55:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tui_26132/03_2026/7tui_26132.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tui_26132/03_2026/7tui_26132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tui_26132/03_2026/7tui_26132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tui_26132/03_2026/7tui_26132.map" model { file = "/net/cci-nas-00/data/ceres_data/7tui_26132/03_2026/7tui_26132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tui_26132/03_2026/7tui_26132.cif" } resolution = 2.66 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= 0.009 sd= 0.273 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 99 5.16 5 C 17478 2.51 5 N 4563 2.21 5 O 5239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27380 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1433, 11295 Classifications: {'peptide': 1433} Link IDs: {'PTRANS': 56, 'TRANS': 1376} Chain breaks: 3 Chain: "B" Number of atoms: 16054 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2033, 16044 Classifications: {'peptide': 2033} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 107, 'TRANS': 1924} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 2033, 16044 Classifications: {'peptide': 2033} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 107, 'TRANS': 1924} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 16400 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS B 727 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 727 " occ=0.50 Time building chain proxies: 8.49, per 1000 atoms: 0.31 Number of scatterers: 27380 At special positions: 0 Unit cell: (202.91, 157.59, 170.98, 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 99 16.00 P 1 15.00 O 5239 8.00 N 4563 7.00 C 17478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.8 seconds 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6460 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 28 sheets defined 46.7% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 3.521A pdb=" N GLU A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 325 through 348 Processing helix chain 'A' and resid 353 through 382 removed outlier: 3.514A pdb=" N ALA A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 394 through 398 removed outlier: 3.778A pdb=" N SER A 398 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.621A pdb=" N ARG A 409 " --> pdb=" O TRP A 405 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.811A pdb=" N ILE A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 456 removed outlier: 3.603A pdb=" N LYS A 448 " --> pdb=" O PRO A 444 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 461 removed outlier: 3.516A pdb=" N LYS A 461 " --> pdb=" O PRO A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 458 through 461' Processing helix chain 'A' and resid 462 through 483 removed outlier: 3.591A pdb=" N LYS A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 690 through 702 removed outlier: 3.521A pdb=" N LEU A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 729 removed outlier: 3.564A pdb=" N THR A 718 " --> pdb=" O SER A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 757 removed outlier: 3.578A pdb=" N ALA A 750 " --> pdb=" O GLN A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 788 through 799 Processing helix chain 'A' and resid 801 through 813 Processing helix chain 'A' and resid 838 through 845 removed outlier: 3.611A pdb=" N SER A 845 " --> pdb=" O GLU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.381A pdb=" N TYR A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 883 No H-bonds generated for 'chain 'A' and resid 881 through 883' Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.623A pdb=" N ILE A 933 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 974 removed outlier: 3.910A pdb=" N ILE A 953 " --> pdb=" O GLU A 949 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ASN A 972 " --> pdb=" O VAL A 968 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 978 removed outlier: 3.695A pdb=" N SER A 978 " --> pdb=" O ALA A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 975 through 978' Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.657A pdb=" N GLN A1003 " --> pdb=" O ASP A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1041 Processing helix chain 'A' and resid 1045 through 1056 Processing helix chain 'A' and resid 1084 through 1099 removed outlier: 4.367A pdb=" N LYS A1089 " --> pdb=" O GLU A1085 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU A1094 " --> pdb=" O SER A1090 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1110 Processing helix chain 'A' and resid 1114 through 1117 Processing helix chain 'A' and resid 1136 through 1148 Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1208 through 1225 removed outlier: 3.502A pdb=" N LEU A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1236 Processing helix chain 'A' and resid 1238 through 1240 No H-bonds generated for 'chain 'A' and resid 1238 through 1240' Processing helix chain 'A' and resid 1252 through 1261 Processing helix chain 'A' and resid 1272 through 1277 Processing helix chain 'A' and resid 1280 through 1290 Processing helix chain 'A' and resid 1302 through 1306 removed outlier: 3.640A pdb=" N THR A1306 " --> pdb=" O ALA A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1320 Processing helix chain 'A' and resid 1335 through 1345 Processing helix chain 'A' and resid 1350 through 1357 Processing helix chain 'A' and resid 1389 through 1396 Processing helix chain 'A' and resid 1422 through 1429 Processing helix chain 'A' and resid 1439 through 1442 removed outlier: 3.644A pdb=" N LEU A1442 " --> pdb=" O SER A1439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1439 through 1442' Processing helix chain 'A' and resid 1443 through 1477 removed outlier: 3.533A pdb=" N GLN A1457 " --> pdb=" O LYS A1453 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN A1470 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A1471 " --> pdb=" O SER A1467 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A1474 " --> pdb=" O GLN A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1513 removed outlier: 4.088A pdb=" N PHE A1489 " --> pdb=" O SER A1485 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A1490 " --> pdb=" O MET A1486 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A1495 " --> pdb=" O LYS A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1532 Processing helix chain 'A' and resid 1536 through 1538 No H-bonds generated for 'chain 'A' and resid 1536 through 1538' Processing helix chain 'A' and resid 1550 through 1568 removed outlier: 3.698A pdb=" N LYS A1555 " --> pdb=" O VAL A1551 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A1558 " --> pdb=" O ASP A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1586 Processing helix chain 'A' and resid 1591 through 1607 Processing helix chain 'A' and resid 1619 through 1623 Processing helix chain 'A' and resid 1662 through 1665 Processing helix chain 'A' and resid 1670 through 1699 removed outlier: 3.508A pdb=" N THR A1679 " --> pdb=" O GLU A1675 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A1697 " --> pdb=" O HIS A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1714 through 1720 Processing helix chain 'A' and resid 1736 through 1740 removed outlier: 3.505A pdb=" N THR A1739 " --> pdb=" O SER A1736 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A1740 " --> pdb=" O ASP A1737 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1736 through 1740' Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 36 removed outlier: 3.969A pdb=" N LEU B 31 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 32 " --> pdb=" O TYR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.508A pdb=" N PHE B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.891A pdb=" N GLU B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.874A pdb=" N LEU B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 189 removed outlier: 5.895A pdb=" N ASP B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 193 removed outlier: 3.736A pdb=" N ASP B 193 " --> pdb=" O PRO B 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 190 through 193' Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 220 through 243 Proline residue: B 226 - end of helix removed outlier: 4.001A pdb=" N LEU B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 263 through 273 removed outlier: 4.542A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 301 removed outlier: 3.666A pdb=" N TYR B 301 " --> pdb=" O CYS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 3.797A pdb=" N LEU B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 removed outlier: 3.560A pdb=" N GLN B 342 " --> pdb=" O LYS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 384 Processing helix chain 'B' and resid 386 through 394 removed outlier: 4.496A pdb=" N ASP B 390 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B 391 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N SER B 392 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 393 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 394 " --> pdb=" O GLN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 416 through 420 removed outlier: 3.804A pdb=" N LEU B 419 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 433 removed outlier: 4.272A pdb=" N LEU B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 removed outlier: 4.034A pdb=" N LYS B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 492 through 495 Processing helix chain 'B' and resid 496 through 503 removed outlier: 4.106A pdb=" N LEU B 500 " --> pdb=" O GLY B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 4.343A pdb=" N ILE B 533 " --> pdb=" O PHE B 529 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 529 through 534' Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 590 through 599 removed outlier: 3.631A pdb=" N VAL B 594 " --> pdb=" O ASN B 590 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER B 597 " --> pdb=" O ILE B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 611 No H-bonds generated for 'chain 'B' and resid 609 through 611' Processing helix chain 'B' and resid 613 through 628 Processing helix chain 'B' and resid 642 through 660 removed outlier: 3.517A pdb=" N LEU B 646 " --> pdb=" O ASN B 642 " (cutoff:3.500A) Proline residue: B 651 - end of helix Processing helix chain 'B' and resid 674 through 684 removed outlier: 3.929A pdb=" N GLU B 680 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR B 681 " --> pdb=" O VAL B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 710 removed outlier: 3.627A pdb=" N HIS B 710 " --> pdb=" O ILE B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 739 removed outlier: 3.516A pdb=" N GLN B 739 " --> pdb=" O GLN B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 760 through 770 Proline residue: B 766 - end of helix Processing helix chain 'B' and resid 771 through 774 Processing helix chain 'B' and resid 801 through 811 Processing helix chain 'B' and resid 815 through 822 removed outlier: 4.763A pdb=" N GLU B 820 " --> pdb=" O GLN B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 828 No H-bonds generated for 'chain 'B' and resid 826 through 828' Processing helix chain 'B' and resid 846 through 859 Processing helix chain 'B' and resid 863 through 886 removed outlier: 4.194A pdb=" N LEU B 868 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASP B 869 " --> pdb=" O ASN B 865 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP B 876 " --> pdb=" O ASN B 872 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N HIS B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 904 Processing helix chain 'B' and resid 905 through 917 Processing helix chain 'B' and resid 927 through 945 Processing helix chain 'B' and resid 957 through 962 removed outlier: 3.671A pdb=" N ASN B 962 " --> pdb=" O ASN B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 975 removed outlier: 4.003A pdb=" N PHE B 967 " --> pdb=" O GLU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 979 Processing helix chain 'B' and resid 984 through 996 Processing helix chain 'B' and resid 1012 through 1019 removed outlier: 3.596A pdb=" N PHE B1016 " --> pdb=" O ARG B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1078 removed outlier: 3.839A pdb=" N GLU B1077 " --> pdb=" O LEU B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1106 Processing helix chain 'B' and resid 1122 through 1132 Processing helix chain 'B' and resid 1136 through 1144 Processing helix chain 'B' and resid 1156 through 1162 removed outlier: 4.095A pdb=" N ASP B1160 " --> pdb=" O ASN B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1177 removed outlier: 3.933A pdb=" N LYS B1177 " --> pdb=" O ASP B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1241 through 1256 Processing helix chain 'B' and resid 1279 through 1285 removed outlier: 3.699A pdb=" N ILE B1283 " --> pdb=" O SER B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1311 through 1321 removed outlier: 3.935A pdb=" N ILE B1315 " --> pdb=" O PHE B1311 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LYS B1318 " --> pdb=" O VAL B1314 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA B1319 " --> pdb=" O ILE B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1322 through 1324 No H-bonds generated for 'chain 'B' and resid 1322 through 1324' Processing helix chain 'B' and resid 1424 through 1433 removed outlier: 4.028A pdb=" N ALA B1428 " --> pdb=" O ALA B1424 " (cutoff:3.500A) Processing helix chain 'B' and resid 1497 through 1507 Processing helix chain 'B' and resid 1536 through 1544 Processing helix chain 'B' and resid 1547 through 1552 removed outlier: 3.984A pdb=" N VAL B1551 " --> pdb=" O ASN B1547 " (cutoff:3.500A) Processing helix chain 'B' and resid 1552 through 1559 Processing helix chain 'B' and resid 1567 through 1579 Processing helix chain 'B' and resid 1664 through 1671 Processing helix chain 'B' and resid 1671 through 1690 Processing helix chain 'B' and resid 1692 through 1699 Processing helix chain 'B' and resid 1710 through 1723 removed outlier: 4.042A pdb=" N ASN B1719 " --> pdb=" O ALA B1715 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B1720 " --> pdb=" O ILE B1716 " (cutoff:3.500A) Processing helix chain 'B' and resid 1761 through 1773 Proline residue: B1767 - end of helix Processing helix chain 'B' and resid 1813 through 1828 removed outlier: 4.049A pdb=" N ASP B1817 " --> pdb=" O GLU B1813 " (cutoff:3.500A) Processing helix chain 'B' and resid 1855 through 1860 removed outlier: 3.795A pdb=" N ARG B1860 " --> pdb=" O ASP B1856 " (cutoff:3.500A) Processing helix chain 'B' and resid 1866 through 1871 Processing helix chain 'B' and resid 1892 through 1903 removed outlier: 3.749A pdb=" N VAL B1901 " --> pdb=" O THR B1897 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B1902 " --> pdb=" O LEU B1898 " (cutoff:3.500A) Processing helix chain 'B' and resid 1903 through 1908 removed outlier: 3.953A pdb=" N ILE B1907 " --> pdb=" O ASN B1903 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B1908 " --> pdb=" O VAL B1904 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1903 through 1908' Processing helix chain 'B' and resid 1911 through 1917 removed outlier: 4.073A pdb=" N LEU B1915 " --> pdb=" O ASP B1911 " (cutoff:3.500A) Processing helix chain 'B' and resid 1927 through 1932 removed outlier: 4.087A pdb=" N ILE B1931 " --> pdb=" O HIS B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1934 through 1942 removed outlier: 6.212A pdb=" N LEU B1940 " --> pdb=" O ALA B1936 " (cutoff:3.500A) Processing helix chain 'B' and resid 1990 through 1995 removed outlier: 3.539A pdb=" N LEU B1994 " --> pdb=" O LYS B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 2010 through 2017 removed outlier: 5.188A pdb=" N GLN B2015 " --> pdb=" O GLU B2012 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B2017 " --> pdb=" O PHE B2014 " (cutoff:3.500A) Processing helix chain 'B' and resid 2024 through 2032 removed outlier: 4.230A pdb=" N SER B2028 " --> pdb=" O GLU B2024 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE B2029 " --> pdb=" O LYS B2025 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.505A pdb=" N ILE A 44 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ARG A 43 " --> pdb=" O THR B1650 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL B1652 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 45 " --> pdb=" O VAL B1652 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR B1649 " --> pdb=" O MET B1791 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 399 through 401 removed outlier: 6.447A pdb=" N VAL A 681 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N THR A 709 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL A 683 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR A 680 " --> pdb=" O ALA A 770 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE A 772 " --> pdb=" O TYR A 680 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 682 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 771 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA A 820 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N CYS A 865 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N CYS A 822 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 867 " --> pdb=" O CYS A 822 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU A 824 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL A 922 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 864 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ALA A 924 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY A 866 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET A 923 " --> pdb=" O GLN A 645 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 502 Processing sheet with id=AA5, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA6, first strand: chain 'A' and resid 1242 through 1244 removed outlier: 6.495A pdb=" N SER A1381 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU A1025 " --> pdb=" O SER A1381 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A1383 " --> pdb=" O PHE A1023 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A1023 " --> pdb=" O ILE A1383 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A1385 " --> pdb=" O THR A1021 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL A1018 " --> pdb=" O LEU A1403 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A1658 " --> pdb=" O ALA A1404 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR A1406 " --> pdb=" O GLN A1656 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN A1656 " --> pdb=" O THR A1406 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A1408 " --> pdb=" O GLY A1654 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY A1654 " --> pdb=" O THR A1408 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A1653 " --> pdb=" O GLY A1649 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA A1642 " --> pdb=" O ILE A1540 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A1542 " --> pdb=" O ALA A1642 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLY A1541 " --> pdb=" O PHE A1577 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL A1579 " --> pdb=" O GLY A1541 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA A1543 " --> pdb=" O VAL A1579 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1059 through 1066 Processing sheet with id=AA8, first strand: chain 'A' and resid 1101 through 1104 removed outlier: 4.226A pdb=" N GLY A1101 " --> pdb=" O GLN A1187 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A1187 " --> pdb=" O GLY A1101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1118 through 1125 Processing sheet with id=AB1, first strand: chain 'A' and resid 1133 through 1135 Processing sheet with id=AB2, first strand: chain 'A' and resid 1608 through 1609 Processing sheet with id=AB3, first strand: chain 'A' and resid 1727 through 1729 Processing sheet with id=AB4, first strand: chain 'B' and resid 6 through 11 Processing sheet with id=AB5, first strand: chain 'B' and resid 256 through 259 removed outlier: 6.740A pdb=" N LEU B 146 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR B 258 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA B 148 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 488 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 406 through 407 removed outlier: 5.772A pdb=" N ASN B 363 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER B 367 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE B 355 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N VAL B 473 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 356 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 555 through 558 Processing sheet with id=AB8, first strand: chain 'B' and resid 750 through 751 removed outlier: 5.944A pdb=" N ILE B 715 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS B 689 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 666 " --> pdb=" O HIS B 689 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 634 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 666 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE B 636 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE B 668 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU B 638 " --> pdb=" O ILE B 668 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE B 604 " --> pdb=" O GLY B 635 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASN B 637 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU B 606 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 579 " --> pdb=" O HIS B 603 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N GLU B 605 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B 581 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA B 607 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET B 580 " --> pdb=" O PHE B 788 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 830 through 834 Processing sheet with id=AC1, first strand: chain 'B' and resid 918 through 919 Processing sheet with id=AC2, first strand: chain 'B' and resid 1113 through 1115 removed outlier: 6.444A pdb=" N LEU B1179 " --> pdb=" O GLU B1194 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU B1194 " --> pdb=" O LEU B1179 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B1181 " --> pdb=" O VAL B1192 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL B1192 " --> pdb=" O ILE B1208 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B1196 " --> pdb=" O GLN B1204 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE B1235 " --> pdb=" O ARG B1146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1271 through 1272 Processing sheet with id=AC4, first strand: chain 'B' and resid 1276 through 1277 Processing sheet with id=AC5, first strand: chain 'B' and resid 1413 through 1418 removed outlier: 4.832A pdb=" N THR B1413 " --> pdb=" O SER B1453 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N SER B1453 " --> pdb=" O THR B1413 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B1415 " --> pdb=" O CYS B1451 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS B1451 " --> pdb=" O THR B1415 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU B1452 " --> pdb=" O THR B1468 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR B1468 " --> pdb=" O GLU B1452 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR B1454 " --> pdb=" O ILE B1466 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE B1466 " --> pdb=" O THR B1454 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B1456 " --> pdb=" O SER B1464 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1413 through 1418 removed outlier: 4.832A pdb=" N THR B1413 " --> pdb=" O SER B1453 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N SER B1453 " --> pdb=" O THR B1413 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B1415 " --> pdb=" O CYS B1451 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS B1451 " --> pdb=" O THR B1415 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B1340 " --> pdb=" O GLN B1395 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B1397 " --> pdb=" O HIS B1338 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HIS B1338 " --> pdb=" O LEU B1397 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG B1399 " --> pdb=" O LEU B1336 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU B1336 " --> pdb=" O ARG B1399 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU B1339 " --> pdb=" O PHE B1598 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS B1595 " --> pdb=" O GLU B1641 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B1641 " --> pdb=" O LYS B1595 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN B1630 " --> pdb=" O PRO B1636 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B1644 " --> pdb=" O LYS B1622 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS B1622 " --> pdb=" O ILE B1644 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1382 through 1384 removed outlier: 6.664A pdb=" N ILE B1382 " --> pdb=" O VAL B1389 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B1387 " --> pdb=" O ARG B1384 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1520 through 1521 Processing sheet with id=AC9, first strand: chain 'B' and resid 1703 through 1707 Processing sheet with id=AD1, first strand: chain 'B' and resid 1840 through 1844 removed outlier: 5.778A pdb=" N ALA B1889 " --> pdb=" O ILE B1876 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE B1876 " --> pdb=" O ALA B1889 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP B1891 " --> pdb=" O LEU B1874 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B1874 " --> pdb=" O ASP B1891 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3183 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: 6.93 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8866 1.34 - 1.46: 5491 1.46 - 1.58: 13449 1.58 - 1.70: 3 1.70 - 1.81: 170 Bond restraints: 27979 Sorted by residual: bond pdb=" C4 FMN B2101 " pdb=" C4A FMN B2101 " ideal model delta sigma weight residual 1.485 1.385 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C4A FMN B2101 " pdb=" N5 FMN B2101 " ideal model delta sigma weight residual 1.300 1.378 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" O5' FMN B2101 " pdb=" P FMN B2101 " ideal model delta sigma weight residual 1.676 1.608 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C10 FMN B2101 " pdb=" N1 FMN B2101 " ideal model delta sigma weight residual 1.317 1.377 -0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" C10 FMN B2101 " pdb=" C4A FMN B2101 " ideal model delta sigma weight residual 1.443 1.384 0.059 2.00e-02 2.50e+03 8.83e+00 ... (remaining 27974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 37405 3.02 - 6.04: 454 6.04 - 9.06: 41 9.06 - 12.09: 6 12.09 - 15.11: 3 Bond angle restraints: 37909 Sorted by residual: angle pdb=" C LEU B1969 " pdb=" N MET B1970 " pdb=" CA MET B1970 " ideal model delta sigma weight residual 121.54 134.44 -12.90 1.91e+00 2.74e-01 4.56e+01 angle pdb=" CA PRO A1132 " pdb=" N PRO A1132 " pdb=" CD PRO A1132 " ideal model delta sigma weight residual 112.00 103.18 8.82 1.40e+00 5.10e-01 3.97e+01 angle pdb=" C GLU B2034 " pdb=" CA GLU B2034 " pdb=" CB GLU B2034 " ideal model delta sigma weight residual 117.23 109.28 7.95 1.36e+00 5.41e-01 3.42e+01 angle pdb=" N LYS B 743 " pdb=" CA LYS B 743 " pdb=" C LYS B 743 " ideal model delta sigma weight residual 114.64 106.04 8.60 1.52e+00 4.33e-01 3.20e+01 angle pdb=" C LYS A1298 " pdb=" N THR A1299 " pdb=" CA THR A1299 " ideal model delta sigma weight residual 122.26 116.89 5.37 1.10e+00 8.26e-01 2.39e+01 ... (remaining 37904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 15577 17.51 - 35.03: 1090 35.03 - 52.54: 153 52.54 - 70.06: 18 70.06 - 87.57: 22 Dihedral angle restraints: 16860 sinusoidal: 6801 harmonic: 10059 Sorted by residual: dihedral pdb=" CA MET B1810 " pdb=" C MET B1810 " pdb=" N PRO B1811 " pdb=" CA PRO B1811 " ideal model delta harmonic sigma weight residual -180.00 -147.05 -32.95 0 5.00e+00 4.00e-02 4.34e+01 dihedral pdb=" CA TYR B1929 " pdb=" C TYR B1929 " pdb=" N GLU B1930 " pdb=" CA GLU B1930 " ideal model delta harmonic sigma weight residual 180.00 148.60 31.40 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA LYS B1982 " pdb=" C LYS B1982 " pdb=" N LYS B1983 " pdb=" CA LYS B1983 " ideal model delta harmonic sigma weight residual -180.00 -148.77 -31.23 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 16857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3091 0.051 - 0.102: 948 0.102 - 0.154: 158 0.154 - 0.205: 18 0.205 - 0.256: 7 Chirality restraints: 4222 Sorted by residual: chirality pdb=" CB ILE B1786 " pdb=" CA ILE B1786 " pdb=" CG1 ILE B1786 " pdb=" CG2 ILE B1786 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR A 709 " pdb=" CA THR A 709 " pdb=" OG1 THR A 709 " pdb=" CG2 THR A 709 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO B1477 " pdb=" N PRO B1477 " pdb=" C PRO B1477 " pdb=" CB PRO B1477 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4219 not shown) Planarity restraints: 4879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1131 " 0.070 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A1132 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A1132 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A1132 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B2005 " 0.051 5.00e-02 4.00e+02 7.64e-02 9.34e+00 pdb=" N PRO B2006 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B2006 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B2006 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B1120 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.18e+00 pdb=" N PRO B1121 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO B1121 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B1121 " -0.043 5.00e-02 4.00e+02 ... (remaining 4876 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 359 2.61 - 3.18: 24797 3.18 - 3.75: 44117 3.75 - 4.33: 62640 4.33 - 4.90: 100274 Nonbonded interactions: 232187 Sorted by model distance: nonbonded pdb=" OG1 THR B1535 " pdb=" OE1 GLU B1537 " model vdw 2.034 3.040 nonbonded pdb=" O LEU B2002 " pdb=" OG1 THR B2003 " model vdw 2.098 3.040 nonbonded pdb=" OD1 ASP A1076 " pdb=" OH TYR A1092 " model vdw 2.100 3.040 nonbonded pdb=" OD2 ASP A1013 " pdb=" OG SER A1506 " model vdw 2.102 3.040 nonbonded pdb=" O PHE A 35 " pdb=" OG1 THR A 41 " model vdw 2.103 3.040 ... (remaining 232182 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.760 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 27979 Z= 0.230 Angle : 0.876 15.108 37909 Z= 0.507 Chirality : 0.049 0.256 4222 Planarity : 0.006 0.101 4879 Dihedral : 12.325 87.574 10400 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.83 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.61 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 3459 helix: -0.73 (0.14), residues: 1355 sheet: -1.69 (0.25), residues: 420 loop : -1.68 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 470 TYR 0.039 0.002 TYR B1777 PHE 0.029 0.002 PHE B1421 TRP 0.036 0.002 TRP B 719 HIS 0.015 0.002 HIS B 842 Details of bonding type rmsd covalent geometry : bond 0.00499 (27979) covalent geometry : angle 0.87568 (37909) hydrogen bonds : bond 0.18520 ( 1134) hydrogen bonds : angle 7.83987 ( 3183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 522 GLU cc_start: 0.7001 (mp0) cc_final: 0.6772 (mp0) REVERT: A 888 ILE cc_start: 0.7949 (mt) cc_final: 0.7716 (OUTLIER) REVERT: A 1138 GLU cc_start: 0.7538 (pt0) cc_final: 0.7319 (pt0) REVERT: A 1261 LYS cc_start: 0.5438 (mttp) cc_final: 0.4693 (ttmt) REVERT: B 387 MET cc_start: 0.2826 (tpp) cc_final: 0.2540 (mmt) REVERT: B 1160 ASP cc_start: 0.7657 (m-30) cc_final: 0.7390 (m-30) REVERT: B 1607 THR cc_start: 0.8226 (t) cc_final: 0.8022 (m) REVERT: B 1791 MET cc_start: 0.4435 (mpp) cc_final: 0.4149 (mpp) outliers start: 0 outliers final: 1 residues processed: 436 average time/residue: 0.7403 time to fit residues: 368.8967 Evaluate side-chains 264 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 HIS A 339 GLN A 434 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1450 GLN A1556 ASN B 363 ASN B 415 HIS ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN B 689 HIS ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN B1370 GLN B1536 ASN B1567 HIS B1669 ASN B1827 GLN B1868 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.244240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.180538 restraints weight = 54204.010| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 3.50 r_work: 0.3859 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 27979 Z= 0.147 Angle : 0.696 12.806 37909 Z= 0.363 Chirality : 0.047 0.247 4222 Planarity : 0.005 0.077 4879 Dihedral : 5.509 55.776 3730 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.77 % Favored : 92.82 % Rotamer: Outliers : 1.57 % Allowed : 10.07 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.14), residues: 3459 helix: -0.10 (0.14), residues: 1363 sheet: -1.77 (0.24), residues: 448 loop : -1.57 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 470 TYR 0.026 0.001 TYR B1777 PHE 0.028 0.002 PHE B1516 TRP 0.027 0.002 TRP B 719 HIS 0.010 0.001 HIS B1614 Details of bonding type rmsd covalent geometry : bond 0.00332 (27979) covalent geometry : angle 0.69610 (37909) hydrogen bonds : bond 0.04398 ( 1134) hydrogen bonds : angle 5.79229 ( 3183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 328 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.0708 (mmp) cc_final: 0.0466 (mmp) REVERT: A 330 THR cc_start: 0.8131 (m) cc_final: 0.7651 (m) REVERT: A 334 LYS cc_start: 0.5932 (tptt) cc_final: 0.4764 (mmtp) REVERT: A 352 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7472 (mp) REVERT: A 390 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7285 (mm-40) REVERT: A 439 MET cc_start: 0.8444 (ptm) cc_final: 0.7865 (mtp) REVERT: A 494 ARG cc_start: 0.7751 (tpt-90) cc_final: 0.7227 (tpp-160) REVERT: A 782 ASN cc_start: 0.8404 (m-40) cc_final: 0.8191 (m110) REVERT: A 923 MET cc_start: 0.8195 (tpt) cc_final: 0.7947 (tpt) REVERT: A 1009 GLU cc_start: 0.8316 (tt0) cc_final: 0.8089 (tt0) REVERT: A 1013 ASP cc_start: 0.7593 (t0) cc_final: 0.7386 (t0) REVERT: A 1094 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6713 (tm-30) REVERT: A 1127 GLN cc_start: 0.7423 (mm-40) cc_final: 0.6695 (mp10) REVERT: A 1138 GLU cc_start: 0.8004 (pt0) cc_final: 0.7719 (pt0) REVERT: A 1261 LYS cc_start: 0.5459 (mttp) cc_final: 0.4301 (ttmt) REVERT: A 1376 MET cc_start: 0.8414 (tpp) cc_final: 0.8203 (tpp) REVERT: A 1445 GLU cc_start: 0.7645 (tp30) cc_final: 0.7432 (tp30) REVERT: A 1500 GLU cc_start: 0.6834 (tp30) cc_final: 0.6491 (mt-10) REVERT: A 1518 LYS cc_start: 0.5791 (pmtt) cc_final: 0.5342 (pmtt) REVERT: A 1626 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: A 1680 LYS cc_start: 0.8573 (mttt) cc_final: 0.8365 (mttp) REVERT: A 1707 LYS cc_start: 0.7769 (tppt) cc_final: 0.7314 (tttt) REVERT: B 329 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6494 (mtp180) REVERT: B 387 MET cc_start: 0.3331 (tpp) cc_final: 0.2588 (mpp) REVERT: B 592 ASP cc_start: 0.6936 (m-30) cc_final: 0.6727 (m-30) REVERT: B 818 GLN cc_start: 0.6899 (mt0) cc_final: 0.6575 (mt0) REVERT: B 866 LYS cc_start: 0.7866 (ptmt) cc_final: 0.7203 (tttm) REVERT: B 980 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7579 (mttt) REVERT: B 1160 ASP cc_start: 0.8033 (m-30) cc_final: 0.7707 (m-30) REVERT: B 1240 GLU cc_start: 0.7200 (pp20) cc_final: 0.6721 (mp0) REVERT: B 1387 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7706 (mttm) REVERT: B 1436 PHE cc_start: 0.8775 (t80) cc_final: 0.8419 (t80) REVERT: B 1576 ARG cc_start: 0.6847 (ttt-90) cc_final: 0.6406 (ttt180) REVERT: B 1607 THR cc_start: 0.8247 (t) cc_final: 0.7924 (m) REVERT: B 1617 MET cc_start: 0.4581 (mpt) cc_final: 0.4181 (mtt) REVERT: B 1773 GLU cc_start: 0.5594 (mt-10) cc_final: 0.4902 (mt-10) REVERT: B 1791 MET cc_start: 0.3648 (mpp) cc_final: 0.3255 (mpp) outliers start: 47 outliers final: 12 residues processed: 353 average time/residue: 0.6749 time to fit residues: 276.5284 Evaluate side-chains 292 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1626 GLU Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 980 LYS Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1387 LYS Chi-restraints excluded: chain B residue 1446 VAL Chi-restraints excluded: chain B residue 1810 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 294 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 143 optimal weight: 40.0000 chunk 231 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN A 904 ASN A 918 GLN A1016 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1450 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN ** B1043 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1066 HIS B1550 HIS B1669 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.242249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.179008 restraints weight = 54236.296| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 3.75 r_work: 0.3871 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27979 Z= 0.147 Angle : 0.657 11.858 37909 Z= 0.341 Chirality : 0.046 0.238 4222 Planarity : 0.005 0.053 4879 Dihedral : 5.390 56.604 3730 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.60 % Favored : 93.08 % Rotamer: Outliers : 1.97 % Allowed : 12.07 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.14), residues: 3459 helix: 0.09 (0.14), residues: 1367 sheet: -1.77 (0.24), residues: 455 loop : -1.55 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1072 TYR 0.024 0.002 TYR B1777 PHE 0.030 0.002 PHE B1516 TRP 0.022 0.002 TRP B 648 HIS 0.008 0.001 HIS B 842 Details of bonding type rmsd covalent geometry : bond 0.00341 (27979) covalent geometry : angle 0.65658 (37909) hydrogen bonds : bond 0.04096 ( 1134) hydrogen bonds : angle 5.47885 ( 3183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 308 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 THR cc_start: 0.8204 (m) cc_final: 0.7713 (m) REVERT: A 334 LYS cc_start: 0.6343 (tptt) cc_final: 0.4709 (mmtp) REVERT: A 352 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7643 (mp) REVERT: A 390 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7313 (mm-40) REVERT: A 439 MET cc_start: 0.8496 (ptm) cc_final: 0.8195 (mtp) REVERT: A 736 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8484 (mp) REVERT: A 799 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8414 (tm) REVERT: A 812 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7788 (mmmt) REVERT: A 901 MET cc_start: 0.7910 (tpt) cc_final: 0.7295 (tpt) REVERT: A 1009 GLU cc_start: 0.8343 (tt0) cc_final: 0.8118 (tt0) REVERT: A 1094 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6979 (tm-30) REVERT: A 1116 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8200 (mttp) REVERT: A 1127 GLN cc_start: 0.7592 (mm-40) cc_final: 0.6695 (mp10) REVERT: A 1138 GLU cc_start: 0.8043 (pt0) cc_final: 0.7780 (pt0) REVERT: A 1261 LYS cc_start: 0.5791 (mttp) cc_final: 0.4315 (ttmt) REVERT: A 1376 MET cc_start: 0.8697 (tpp) cc_final: 0.8354 (tpp) REVERT: A 1445 GLU cc_start: 0.7769 (tp30) cc_final: 0.7556 (tp30) REVERT: A 1500 GLU cc_start: 0.6953 (tp30) cc_final: 0.6469 (mt-10) REVERT: A 1579 VAL cc_start: 0.8225 (m) cc_final: 0.7971 (t) REVERT: A 1680 LYS cc_start: 0.8599 (mttt) cc_final: 0.8372 (mttp) REVERT: B 387 MET cc_start: 0.3450 (tpp) cc_final: 0.2671 (mpp) REVERT: B 584 MET cc_start: 0.7665 (mtm) cc_final: 0.7236 (mtm) REVERT: B 592 ASP cc_start: 0.7031 (m-30) cc_final: 0.6804 (m-30) REVERT: B 818 GLN cc_start: 0.6761 (mt0) cc_final: 0.6405 (mt0) REVERT: B 933 MET cc_start: 0.8459 (ttt) cc_final: 0.8250 (ptm) REVERT: B 980 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7606 (mttt) REVERT: B 1160 ASP cc_start: 0.8065 (m-30) cc_final: 0.7760 (m-30) REVERT: B 1436 PHE cc_start: 0.8751 (t80) cc_final: 0.8324 (t80) REVERT: B 1576 ARG cc_start: 0.6993 (ttt-90) cc_final: 0.6454 (ttt180) REVERT: B 1617 MET cc_start: 0.4747 (OUTLIER) cc_final: 0.4198 (mtt) REVERT: B 1773 GLU cc_start: 0.5602 (mt-10) cc_final: 0.4951 (mt-10) REVERT: B 1791 MET cc_start: 0.3899 (mpp) cc_final: 0.3469 (mpp) REVERT: B 1837 ARG cc_start: 0.6646 (ptt90) cc_final: 0.6431 (ptm160) outliers start: 59 outliers final: 18 residues processed: 343 average time/residue: 0.7079 time to fit residues: 281.1536 Evaluate side-chains 300 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 980 LYS Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1390 MET Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1617 MET Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1754 SER Chi-restraints excluded: chain B residue 1810 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 115 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 151 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 132 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1546 HIS B 262 GLN B 363 ASN ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN B1066 HIS B1669 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.243882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.181698 restraints weight = 58143.847| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.87 r_work: 0.3889 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 27979 Z= 0.123 Angle : 0.617 11.532 37909 Z= 0.320 Chirality : 0.045 0.232 4222 Planarity : 0.005 0.050 4879 Dihedral : 5.200 56.574 3730 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.60 % Favored : 93.08 % Rotamer: Outliers : 2.27 % Allowed : 13.27 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3459 helix: 0.28 (0.14), residues: 1368 sheet: -1.66 (0.24), residues: 455 loop : -1.51 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1072 TYR 0.021 0.001 TYR B1777 PHE 0.029 0.002 PHE B1516 TRP 0.021 0.001 TRP B 648 HIS 0.006 0.001 HIS B 842 Details of bonding type rmsd covalent geometry : bond 0.00282 (27979) covalent geometry : angle 0.61714 (37909) hydrogen bonds : bond 0.03630 ( 1134) hydrogen bonds : angle 5.19302 ( 3183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 303 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 THR cc_start: 0.8277 (m) cc_final: 0.7789 (m) REVERT: A 334 LYS cc_start: 0.6376 (tptt) cc_final: 0.4709 (mmtp) REVERT: A 349 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: A 387 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7742 (pttt) REVERT: A 390 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7284 (mm-40) REVERT: A 439 MET cc_start: 0.8275 (ptm) cc_final: 0.7997 (mtp) REVERT: A 499 LYS cc_start: 0.7473 (tptt) cc_final: 0.7149 (mmtt) REVERT: A 674 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7965 (tt) REVERT: A 758 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7824 (pm20) REVERT: A 812 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7666 (mmmt) REVERT: A 1003 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: A 1009 GLU cc_start: 0.8293 (tt0) cc_final: 0.8073 (tt0) REVERT: A 1052 MET cc_start: 0.8625 (mmm) cc_final: 0.8235 (mmm) REVERT: A 1094 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6986 (tm-30) REVERT: A 1127 GLN cc_start: 0.7620 (mm-40) cc_final: 0.6700 (mp10) REVERT: A 1138 GLU cc_start: 0.8126 (pt0) cc_final: 0.7852 (pt0) REVERT: A 1201 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7230 (mm-30) REVERT: A 1261 LYS cc_start: 0.5528 (mttp) cc_final: 0.4217 (ptpt) REVERT: A 1376 MET cc_start: 0.8763 (tpp) cc_final: 0.8363 (tpp) REVERT: A 1445 GLU cc_start: 0.7753 (tp30) cc_final: 0.7497 (tp30) REVERT: A 1500 GLU cc_start: 0.6855 (tp30) cc_final: 0.6478 (mt-10) REVERT: A 1713 GLU cc_start: 0.7341 (mp0) cc_final: 0.7070 (mm-30) REVERT: B 325 MET cc_start: 0.0133 (OUTLIER) cc_final: -0.1225 (mmp) REVERT: B 584 MET cc_start: 0.7786 (mtm) cc_final: 0.7489 (mtm) REVERT: B 592 ASP cc_start: 0.7046 (m-30) cc_final: 0.6818 (m-30) REVERT: B 777 ASN cc_start: 0.7435 (m-40) cc_final: 0.7204 (m-40) REVERT: B 818 GLN cc_start: 0.6821 (mt0) cc_final: 0.6187 (mp10) REVERT: B 933 MET cc_start: 0.8382 (ttt) cc_final: 0.8149 (ptm) REVERT: B 980 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7580 (mttt) REVERT: B 1160 ASP cc_start: 0.8051 (m-30) cc_final: 0.7711 (m-30) REVERT: B 1436 PHE cc_start: 0.8720 (t80) cc_final: 0.8280 (t80) REVERT: B 1576 ARG cc_start: 0.6959 (ttt-90) cc_final: 0.6465 (ttt90) REVERT: B 1617 MET cc_start: 0.4329 (OUTLIER) cc_final: 0.3580 (mtt) REVERT: B 1702 ASN cc_start: 0.8053 (m110) cc_final: 0.7628 (m-40) REVERT: B 1773 GLU cc_start: 0.5604 (mt-10) cc_final: 0.4863 (mt-10) REVERT: B 1791 MET cc_start: 0.3991 (mpp) cc_final: 0.3612 (mpp) outliers start: 68 outliers final: 20 residues processed: 341 average time/residue: 0.6481 time to fit residues: 260.7255 Evaluate side-chains 298 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 1003 GLN Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1201 GLU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 980 LYS Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1446 VAL Chi-restraints excluded: chain B residue 1617 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 160 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 301 optimal weight: 0.3980 chunk 262 optimal weight: 10.0000 chunk 330 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 322 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN A 904 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN B1066 HIS B1184 ASN ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1669 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1965 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.241816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176349 restraints weight = 51469.267| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.11 r_work: 0.3856 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 27979 Z= 0.141 Angle : 0.634 11.641 37909 Z= 0.327 Chirality : 0.045 0.230 4222 Planarity : 0.005 0.048 4879 Dihedral : 5.224 57.745 3730 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.57 % Favored : 93.14 % Rotamer: Outliers : 2.80 % Allowed : 14.17 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3459 helix: 0.35 (0.14), residues: 1371 sheet: -1.58 (0.24), residues: 449 loop : -1.43 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 470 TYR 0.022 0.002 TYR B 59 PHE 0.028 0.002 PHE A 35 TRP 0.020 0.001 TRP B 648 HIS 0.006 0.001 HIS B 842 Details of bonding type rmsd covalent geometry : bond 0.00329 (27979) covalent geometry : angle 0.63377 (37909) hydrogen bonds : bond 0.03676 ( 1134) hydrogen bonds : angle 5.16452 ( 3183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 290 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 GLU cc_start: 0.7543 (tt0) cc_final: 0.7098 (tp30) REVERT: A 334 LYS cc_start: 0.6484 (tptt) cc_final: 0.4729 (mmtt) REVERT: A 352 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7781 (mp) REVERT: A 390 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7374 (mm-40) REVERT: A 396 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7880 (pp) REVERT: A 434 GLN cc_start: 0.7553 (pt0) cc_final: 0.7260 (mt0) REVERT: A 439 MET cc_start: 0.8308 (ptm) cc_final: 0.8065 (mtp) REVERT: A 668 SER cc_start: 0.7881 (m) cc_final: 0.7594 (t) REVERT: A 674 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7984 (tt) REVERT: A 758 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7828 (pm20) REVERT: A 799 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8384 (tm) REVERT: A 812 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7763 (mmmt) REVERT: A 901 MET cc_start: 0.7825 (tpt) cc_final: 0.7296 (tpt) REVERT: A 944 ARG cc_start: 0.7606 (ptp-110) cc_final: 0.7241 (ttm110) REVERT: A 1003 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: A 1009 GLU cc_start: 0.8360 (tt0) cc_final: 0.8107 (tt0) REVERT: A 1052 MET cc_start: 0.8676 (mmm) cc_final: 0.8187 (mmm) REVERT: A 1094 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7193 (tm-30) REVERT: A 1116 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8162 (mttp) REVERT: A 1127 GLN cc_start: 0.7698 (mm-40) cc_final: 0.6799 (mp10) REVERT: A 1138 GLU cc_start: 0.8187 (pt0) cc_final: 0.7885 (pt0) REVERT: A 1261 LYS cc_start: 0.5779 (mttp) cc_final: 0.4241 (ttmt) REVERT: A 1376 MET cc_start: 0.8880 (tpp) cc_final: 0.8538 (tpp) REVERT: A 1474 GLU cc_start: 0.5588 (OUTLIER) cc_final: 0.5270 (pm20) REVERT: A 1500 GLU cc_start: 0.7022 (tp30) cc_final: 0.6649 (mt-10) REVERT: A 1518 LYS cc_start: 0.5809 (pmtt) cc_final: 0.4581 (mmtt) REVERT: A 1579 VAL cc_start: 0.8248 (m) cc_final: 0.8005 (t) REVERT: A 1626 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: B 325 MET cc_start: 0.0206 (OUTLIER) cc_final: -0.0972 (mmp) REVERT: B 592 ASP cc_start: 0.7131 (m-30) cc_final: 0.6889 (m-30) REVERT: B 818 GLN cc_start: 0.6858 (mt0) cc_final: 0.6273 (mp10) REVERT: B 825 LYS cc_start: 0.6011 (pptt) cc_final: 0.5765 (pptt) REVERT: B 866 LYS cc_start: 0.7929 (ptpt) cc_final: 0.7186 (tttm) REVERT: B 933 MET cc_start: 0.8425 (ttt) cc_final: 0.8186 (ptm) REVERT: B 980 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7585 (mttt) REVERT: B 1160 ASP cc_start: 0.8059 (m-30) cc_final: 0.7769 (m-30) REVERT: B 1436 PHE cc_start: 0.8733 (t80) cc_final: 0.8281 (t80) REVERT: B 1576 ARG cc_start: 0.7005 (ttt-90) cc_final: 0.6612 (ttt180) REVERT: B 1617 MET cc_start: 0.4549 (OUTLIER) cc_final: 0.3564 (mtt) REVERT: B 1773 GLU cc_start: 0.5685 (mt-10) cc_final: 0.4917 (mt-10) REVERT: B 1791 MET cc_start: 0.4088 (mpp) cc_final: 0.3722 (mpp) REVERT: B 1892 LEU cc_start: 0.7201 (mt) cc_final: 0.6797 (mt) outliers start: 84 outliers final: 29 residues processed: 349 average time/residue: 0.6635 time to fit residues: 270.5463 Evaluate side-chains 305 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1003 GLN Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1626 GLU Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 980 LYS Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1617 MET Chi-restraints excluded: chain B residue 1685 PHE Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1754 SER Chi-restraints excluded: chain B residue 1810 MET Chi-restraints excluded: chain B residue 1877 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 308 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 296 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 295 optimal weight: 0.0170 chunk 168 optimal weight: 8.9990 chunk 270 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN A1187 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 HIS ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1669 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.244208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.181881 restraints weight = 62003.352| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 3.62 r_work: 0.3899 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 27979 Z= 0.116 Angle : 0.603 12.608 37909 Z= 0.310 Chirality : 0.044 0.228 4222 Planarity : 0.004 0.052 4879 Dihedral : 5.067 58.560 3730 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.66 % Rotamer: Outliers : 2.37 % Allowed : 15.37 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3459 helix: 0.48 (0.14), residues: 1373 sheet: -1.60 (0.24), residues: 452 loop : -1.38 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 470 TYR 0.018 0.001 TYR B1777 PHE 0.047 0.002 PHE B 62 TRP 0.021 0.001 TRP B 648 HIS 0.005 0.001 HIS B 842 Details of bonding type rmsd covalent geometry : bond 0.00265 (27979) covalent geometry : angle 0.60347 (37909) hydrogen bonds : bond 0.03420 ( 1134) hydrogen bonds : angle 5.02248 ( 3183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 300 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 330 THR cc_start: 0.8323 (m) cc_final: 0.7774 (m) REVERT: A 332 GLU cc_start: 0.7652 (tt0) cc_final: 0.7189 (tp30) REVERT: A 334 LYS cc_start: 0.6427 (tptt) cc_final: 0.4762 (mmtp) REVERT: A 352 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7871 (mp) REVERT: A 387 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7807 (pttt) REVERT: A 390 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7340 (mm-40) REVERT: A 396 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7834 (pp) REVERT: A 653 GLU cc_start: 0.7757 (pt0) cc_final: 0.6951 (pm20) REVERT: A 758 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7877 (pm20) REVERT: A 799 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8345 (tm) REVERT: A 812 LYS cc_start: 0.7963 (mmtt) cc_final: 0.7660 (mmmt) REVERT: A 901 MET cc_start: 0.7674 (tpt) cc_final: 0.7274 (tpt) REVERT: A 1003 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: A 1009 GLU cc_start: 0.8289 (tt0) cc_final: 0.8052 (tt0) REVERT: A 1039 GLU cc_start: 0.8054 (tt0) cc_final: 0.7729 (tt0) REVERT: A 1052 MET cc_start: 0.8650 (mmm) cc_final: 0.8184 (mmm) REVERT: A 1127 GLN cc_start: 0.7705 (mm-40) cc_final: 0.6786 (mp10) REVERT: A 1138 GLU cc_start: 0.8205 (pt0) cc_final: 0.7921 (pt0) REVERT: A 1261 LYS cc_start: 0.5549 (mttp) cc_final: 0.4264 (ptpt) REVERT: A 1376 MET cc_start: 0.8836 (tpp) cc_final: 0.8580 (tpp) REVERT: A 1474 GLU cc_start: 0.5617 (OUTLIER) cc_final: 0.5306 (pm20) REVERT: A 1500 GLU cc_start: 0.7013 (tp30) cc_final: 0.6682 (mt-10) REVERT: A 1518 LYS cc_start: 0.5873 (pmtt) cc_final: 0.4599 (mmtt) REVERT: A 1564 MET cc_start: 0.8018 (ptm) cc_final: 0.7785 (ptp) REVERT: A 1579 VAL cc_start: 0.8181 (m) cc_final: 0.7913 (t) REVERT: A 1616 ASP cc_start: 0.7272 (m-30) cc_final: 0.6997 (p0) REVERT: A 1713 GLU cc_start: 0.7248 (mp0) cc_final: 0.7000 (mm-30) REVERT: B 325 MET cc_start: 0.0264 (OUTLIER) cc_final: -0.0886 (mmp) REVERT: B 592 ASP cc_start: 0.7095 (m-30) cc_final: 0.6865 (m-30) REVERT: B 818 GLN cc_start: 0.6878 (mt0) cc_final: 0.6265 (mp10) REVERT: B 831 ILE cc_start: 0.8068 (pt) cc_final: 0.7807 (pp) REVERT: B 887 GLN cc_start: 0.7127 (mt0) cc_final: 0.6886 (mt0) REVERT: B 980 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7585 (mttt) REVERT: B 1160 ASP cc_start: 0.8024 (m-30) cc_final: 0.7789 (m-30) REVERT: B 1436 PHE cc_start: 0.8694 (t80) cc_final: 0.8257 (t80) REVERT: B 1576 ARG cc_start: 0.6891 (ttt-90) cc_final: 0.6538 (ttt90) REVERT: B 1605 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7487 (m-40) REVERT: B 1617 MET cc_start: 0.4419 (OUTLIER) cc_final: 0.2945 (mtt) REVERT: B 1665 MET cc_start: 0.8169 (mmp) cc_final: 0.7709 (mmp) REVERT: B 1773 GLU cc_start: 0.5719 (mt-10) cc_final: 0.4939 (mt-10) REVERT: B 1791 MET cc_start: 0.3866 (mpp) cc_final: 0.3497 (mpp) REVERT: B 1892 LEU cc_start: 0.7189 (mt) cc_final: 0.6798 (mt) outliers start: 71 outliers final: 28 residues processed: 347 average time/residue: 0.6570 time to fit residues: 266.9696 Evaluate side-chains 315 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 1003 GLN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1331 TYR Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1628 VAL Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 980 LYS Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1605 ASN Chi-restraints excluded: chain B residue 1617 MET Chi-restraints excluded: chain B residue 1685 PHE Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1754 SER Chi-restraints excluded: chain B residue 1877 VAL Chi-restraints excluded: chain B residue 1965 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 72 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 217 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 188 optimal weight: 30.0000 chunk 112 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 252 optimal weight: 30.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN B1066 HIS ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.243142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.178154 restraints weight = 51788.758| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 3.23 r_work: 0.3865 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 27979 Z= 0.123 Angle : 0.607 10.280 37909 Z= 0.311 Chirality : 0.045 0.272 4222 Planarity : 0.004 0.049 4879 Dihedral : 5.007 58.294 3730 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.37 % Favored : 93.40 % Rotamer: Outliers : 2.57 % Allowed : 15.93 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3459 helix: 0.50 (0.14), residues: 1379 sheet: -1.54 (0.24), residues: 442 loop : -1.36 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 470 TYR 0.023 0.001 TYR B1114 PHE 0.034 0.002 PHE B 62 TRP 0.027 0.001 TRP B1137 HIS 0.004 0.001 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00289 (27979) covalent geometry : angle 0.60700 (37909) hydrogen bonds : bond 0.03422 ( 1134) hydrogen bonds : angle 4.98753 ( 3183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 332 GLU cc_start: 0.7675 (tt0) cc_final: 0.7186 (tp30) REVERT: A 334 LYS cc_start: 0.6489 (tptt) cc_final: 0.4711 (mmtt) REVERT: A 352 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7887 (mp) REVERT: A 387 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7818 (pttt) REVERT: A 390 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7330 (mm-40) REVERT: A 396 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7831 (pp) REVERT: A 653 GLU cc_start: 0.7758 (pt0) cc_final: 0.6948 (pm20) REVERT: A 668 SER cc_start: 0.7866 (m) cc_final: 0.7637 (t) REVERT: A 758 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7815 (pm20) REVERT: A 799 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8387 (tm) REVERT: A 812 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7668 (mmmt) REVERT: A 944 ARG cc_start: 0.7626 (ptp-110) cc_final: 0.7257 (ttm110) REVERT: A 1003 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: A 1009 GLU cc_start: 0.8336 (tt0) cc_final: 0.8098 (tt0) REVERT: A 1039 GLU cc_start: 0.8070 (tt0) cc_final: 0.7830 (tt0) REVERT: A 1052 MET cc_start: 0.8663 (mmm) cc_final: 0.8168 (mmm) REVERT: A 1127 GLN cc_start: 0.7573 (mm-40) cc_final: 0.6747 (mp10) REVERT: A 1138 GLU cc_start: 0.8169 (pt0) cc_final: 0.7852 (pt0) REVERT: A 1261 LYS cc_start: 0.5616 (mttp) cc_final: 0.4295 (ptpt) REVERT: A 1376 MET cc_start: 0.8839 (tpp) cc_final: 0.8551 (tpp) REVERT: A 1474 GLU cc_start: 0.5618 (OUTLIER) cc_final: 0.5365 (pm20) REVERT: A 1500 GLU cc_start: 0.7043 (tp30) cc_final: 0.6740 (mt-10) REVERT: A 1518 LYS cc_start: 0.5696 (pmtt) cc_final: 0.4502 (mmtt) REVERT: A 1564 MET cc_start: 0.7979 (ptm) cc_final: 0.7687 (ptp) REVERT: A 1579 VAL cc_start: 0.8240 (m) cc_final: 0.8000 (t) REVERT: A 1616 ASP cc_start: 0.7373 (m-30) cc_final: 0.7165 (p0) REVERT: A 1626 GLU cc_start: 0.7982 (mp0) cc_final: 0.7613 (pm20) REVERT: A 1707 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7309 (tttt) REVERT: B 325 MET cc_start: 0.0412 (OUTLIER) cc_final: -0.0681 (mmp) REVERT: B 592 ASP cc_start: 0.7058 (m-30) cc_final: 0.6827 (m-30) REVERT: B 701 SER cc_start: 0.7180 (m) cc_final: 0.6788 (p) REVERT: B 818 GLN cc_start: 0.6943 (mt0) cc_final: 0.6281 (mp10) REVERT: B 831 ILE cc_start: 0.8080 (pt) cc_final: 0.7814 (pp) REVERT: B 866 LYS cc_start: 0.7981 (ptpt) cc_final: 0.7229 (tttm) REVERT: B 980 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7543 (mttt) REVERT: B 1160 ASP cc_start: 0.8094 (m-30) cc_final: 0.7871 (m-30) REVERT: B 1436 PHE cc_start: 0.8667 (t80) cc_final: 0.8134 (t80) REVERT: B 1605 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7556 (m-40) REVERT: B 1617 MET cc_start: 0.4297 (mpt) cc_final: 0.3974 (mpt) REVERT: B 1750 TYR cc_start: 0.8029 (t80) cc_final: 0.7519 (t80) REVERT: B 1773 GLU cc_start: 0.5830 (mt-10) cc_final: 0.5053 (mt-10) REVERT: B 1791 MET cc_start: 0.3927 (mpp) cc_final: 0.3571 (mpp) REVERT: B 1892 LEU cc_start: 0.7223 (mt) cc_final: 0.6800 (mt) outliers start: 77 outliers final: 32 residues processed: 335 average time/residue: 0.6399 time to fit residues: 252.1219 Evaluate side-chains 314 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1003 GLN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1331 TYR Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1628 VAL Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 980 LYS Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1605 ASN Chi-restraints excluded: chain B residue 1685 PHE Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1754 SER Chi-restraints excluded: chain B residue 1877 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 5 optimal weight: 10.0000 chunk 280 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 342 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 456 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN A1187 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN B 734 HIS B 887 GLN B1153 HIS ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1605 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.235563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.169359 restraints weight = 53570.115| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.30 r_work: 0.3755 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27979 Z= 0.260 Angle : 0.750 10.469 37909 Z= 0.387 Chirality : 0.051 0.319 4222 Planarity : 0.005 0.057 4879 Dihedral : 5.519 57.511 3730 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.32 % Favored : 92.45 % Rotamer: Outliers : 2.67 % Allowed : 15.97 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3459 helix: 0.14 (0.14), residues: 1361 sheet: -1.77 (0.23), residues: 455 loop : -1.34 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 470 TYR 0.030 0.002 TYR A 385 PHE 0.031 0.003 PHE B1740 TRP 0.021 0.002 TRP B1137 HIS 0.013 0.002 HIS A1145 Details of bonding type rmsd covalent geometry : bond 0.00620 (27979) covalent geometry : angle 0.74992 (37909) hydrogen bonds : bond 0.04292 ( 1134) hydrogen bonds : angle 5.36338 ( 3183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 310 time to evaluate : 1.032 Fit side-chains REVERT: A 332 GLU cc_start: 0.7685 (tt0) cc_final: 0.7105 (tp30) REVERT: A 334 LYS cc_start: 0.6397 (tptt) cc_final: 0.4572 (mmtt) REVERT: A 352 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8010 (mp) REVERT: A 396 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8008 (pp) REVERT: A 509 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6377 (tp30) REVERT: A 758 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7749 (pm20) REVERT: A 944 ARG cc_start: 0.7539 (ptp-110) cc_final: 0.7131 (ttm110) REVERT: A 1009 GLU cc_start: 0.8365 (tt0) cc_final: 0.8088 (tt0) REVERT: A 1013 ASP cc_start: 0.7478 (t0) cc_final: 0.7220 (t0) REVERT: A 1086 LYS cc_start: 0.7259 (mtmt) cc_final: 0.6884 (mtpm) REVERT: A 1127 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7051 (mp10) REVERT: A 1138 GLU cc_start: 0.8122 (pt0) cc_final: 0.7821 (pt0) REVERT: A 1161 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6672 (mm-30) REVERT: A 1204 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8146 (mp) REVERT: A 1261 LYS cc_start: 0.5902 (mttp) cc_final: 0.4348 (ttmt) REVERT: A 1474 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.5524 (pm20) REVERT: A 1635 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8574 (tp) REVERT: A 1707 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7281 (tmtt) REVERT: B 325 MET cc_start: 0.0153 (OUTLIER) cc_final: -0.0214 (mmm) REVERT: B 553 ARG cc_start: 0.6262 (ttp-110) cc_final: 0.5992 (ttt180) REVERT: B 592 ASP cc_start: 0.7263 (m-30) cc_final: 0.6941 (m-30) REVERT: B 818 GLN cc_start: 0.6885 (mt0) cc_final: 0.6271 (mp10) REVERT: B 825 LYS cc_start: 0.6625 (pptt) cc_final: 0.6313 (pptt) REVERT: B 866 LYS cc_start: 0.8005 (ptpt) cc_final: 0.7317 (tttm) REVERT: B 1160 ASP cc_start: 0.8145 (m-30) cc_final: 0.7890 (m-30) REVERT: B 1358 VAL cc_start: 0.7719 (OUTLIER) cc_final: 0.7506 (t) REVERT: B 1429 VAL cc_start: 0.7868 (t) cc_final: 0.7577 (m) REVERT: B 1436 PHE cc_start: 0.8722 (t80) cc_final: 0.8301 (t80) REVERT: B 1597 ASP cc_start: 0.8033 (p0) cc_final: 0.7741 (p0) REVERT: B 1617 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.4797 (mtt) REVERT: B 1676 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7024 (mm-30) REVERT: B 1740 PHE cc_start: 0.6179 (OUTLIER) cc_final: 0.5652 (m-80) REVERT: B 1750 TYR cc_start: 0.8013 (t80) cc_final: 0.7456 (t80) REVERT: B 1772 MET cc_start: 0.7440 (ppp) cc_final: 0.7218 (pp-130) REVERT: B 1773 GLU cc_start: 0.5746 (mt-10) cc_final: 0.4820 (mt-10) REVERT: B 1892 LEU cc_start: 0.7153 (mt) cc_final: 0.6730 (mt) outliers start: 80 outliers final: 44 residues processed: 367 average time/residue: 0.6686 time to fit residues: 285.8524 Evaluate side-chains 330 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 275 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1120 MET Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1331 TYR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1628 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 980 LYS Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1358 VAL Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1617 MET Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1740 PHE Chi-restraints excluded: chain B residue 1754 SER Chi-restraints excluded: chain B residue 1877 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 267 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 313 optimal weight: 0.9980 chunk 272 optimal weight: 0.9990 chunk 152 optimal weight: 0.0370 chunk 232 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 171 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN A 904 ASN A1187 GLN ** A1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 GLN B 603 HIS B 702 GLN ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1437 HIS B1827 GLN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.240805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.178695 restraints weight = 60080.862| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.14 r_work: 0.3894 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 27979 Z= 0.125 Angle : 0.644 14.986 37909 Z= 0.329 Chirality : 0.045 0.224 4222 Planarity : 0.004 0.052 4879 Dihedral : 5.135 56.122 3730 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.25 % Favored : 93.52 % Rotamer: Outliers : 1.90 % Allowed : 17.37 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3459 helix: 0.38 (0.14), residues: 1366 sheet: -1.58 (0.24), residues: 442 loop : -1.35 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 470 TYR 0.022 0.001 TYR B1777 PHE 0.026 0.002 PHE A 35 TRP 0.023 0.001 TRP B1137 HIS 0.005 0.001 HIS B1614 Details of bonding type rmsd covalent geometry : bond 0.00288 (27979) covalent geometry : angle 0.64436 (37909) hydrogen bonds : bond 0.03537 ( 1134) hydrogen bonds : angle 5.08543 ( 3183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 1.076 Fit side-chains REVERT: A 332 GLU cc_start: 0.7727 (tt0) cc_final: 0.7245 (tp30) REVERT: A 334 LYS cc_start: 0.6504 (tptt) cc_final: 0.4718 (mmtt) REVERT: A 396 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7888 (pp) REVERT: A 501 LYS cc_start: 0.7607 (ptmt) cc_final: 0.7316 (ptpp) REVERT: A 646 LYS cc_start: 0.8456 (tttp) cc_final: 0.8155 (tttp) REVERT: A 653 GLU cc_start: 0.7705 (pt0) cc_final: 0.6984 (pm20) REVERT: A 758 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7816 (pm20) REVERT: A 901 MET cc_start: 0.7567 (tpt) cc_final: 0.7165 (tpt) REVERT: A 1003 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: A 1009 GLU cc_start: 0.8380 (tt0) cc_final: 0.8170 (tt0) REVERT: A 1011 MET cc_start: 0.7967 (tpt) cc_final: 0.7685 (tpp) REVERT: A 1013 ASP cc_start: 0.7356 (t0) cc_final: 0.7096 (t0) REVERT: A 1052 MET cc_start: 0.8615 (mmm) cc_final: 0.8078 (mmm) REVERT: A 1086 LYS cc_start: 0.7182 (mtmt) cc_final: 0.6853 (mtpm) REVERT: A 1127 GLN cc_start: 0.7665 (mm-40) cc_final: 0.6862 (mp10) REVERT: A 1138 GLU cc_start: 0.8182 (pt0) cc_final: 0.7889 (pt0) REVERT: A 1141 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7997 (mt-10) REVERT: A 1161 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6502 (mm-30) REVERT: A 1261 LYS cc_start: 0.5524 (mttp) cc_final: 0.4263 (ptpt) REVERT: A 1474 GLU cc_start: 0.5709 (OUTLIER) cc_final: 0.5470 (pm20) REVERT: A 1518 LYS cc_start: 0.5751 (pmtt) cc_final: 0.4644 (mmtt) REVERT: A 1557 GLU cc_start: 0.7955 (tt0) cc_final: 0.7633 (tt0) REVERT: A 1635 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8472 (tp) REVERT: A 1707 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7265 (tttt) REVERT: B 592 ASP cc_start: 0.7315 (m-30) cc_final: 0.7030 (m-30) REVERT: B 818 GLN cc_start: 0.6939 (mt0) cc_final: 0.6207 (mp-120) REVERT: B 825 LYS cc_start: 0.6210 (pptt) cc_final: 0.5979 (pptt) REVERT: B 831 ILE cc_start: 0.8030 (pt) cc_final: 0.7785 (pp) REVERT: B 980 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7641 (mttt) REVERT: B 1128 ASP cc_start: 0.7529 (m-30) cc_final: 0.7275 (m-30) REVERT: B 1160 ASP cc_start: 0.8032 (m-30) cc_final: 0.7759 (m-30) REVERT: B 1358 VAL cc_start: 0.7756 (OUTLIER) cc_final: 0.7528 (t) REVERT: B 1363 GLU cc_start: 0.7604 (tt0) cc_final: 0.7384 (mt-10) REVERT: B 1385 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7299 (pp20) REVERT: B 1429 VAL cc_start: 0.7866 (t) cc_final: 0.7593 (m) REVERT: B 1597 ASP cc_start: 0.7953 (p0) cc_final: 0.7749 (p0) REVERT: B 1605 ASN cc_start: 0.8105 (m-40) cc_final: 0.7699 (m-40) REVERT: B 1773 GLU cc_start: 0.5716 (mt-10) cc_final: 0.4748 (mt-10) REVERT: B 1791 MET cc_start: 0.4153 (mpp) cc_final: 0.3889 (mpp) REVERT: B 1892 LEU cc_start: 0.7161 (mt) cc_final: 0.6733 (mt) REVERT: B 1970 MET cc_start: 0.0378 (mpm) cc_final: -0.2965 (tmm) outliers start: 57 outliers final: 27 residues processed: 329 average time/residue: 0.6897 time to fit residues: 265.6755 Evaluate side-chains 315 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 1003 GLN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1628 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 980 LYS Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1358 VAL Chi-restraints excluded: chain B residue 1385 GLU Chi-restraints excluded: chain B residue 1390 MET Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1754 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 50 optimal weight: 0.0470 chunk 27 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 225 optimal weight: 0.2980 chunk 222 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 overall best weight: 2.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN A1187 GLN ** A1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.237721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.173636 restraints weight = 56154.622| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 3.41 r_work: 0.3823 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3708 r_free = 0.3708 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27979 Z= 0.165 Angle : 0.669 12.071 37909 Z= 0.343 Chirality : 0.046 0.268 4222 Planarity : 0.005 0.084 4879 Dihedral : 5.185 57.116 3730 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.94 % Favored : 92.82 % Rotamer: Outliers : 1.67 % Allowed : 17.93 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.14), residues: 3459 helix: 0.37 (0.14), residues: 1363 sheet: -1.70 (0.23), residues: 462 loop : -1.30 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 470 TYR 0.023 0.002 TYR B1114 PHE 0.027 0.002 PHE A 35 TRP 0.020 0.002 TRP B1137 HIS 0.007 0.001 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00391 (27979) covalent geometry : angle 0.66947 (37909) hydrogen bonds : bond 0.03705 ( 1134) hydrogen bonds : angle 5.11063 ( 3183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 1.027 Fit side-chains REVERT: A 332 GLU cc_start: 0.7730 (tt0) cc_final: 0.7101 (tp30) REVERT: A 334 LYS cc_start: 0.6544 (tptt) cc_final: 0.4664 (mmtt) REVERT: A 349 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: A 396 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7944 (pp) REVERT: A 509 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6222 (tp30) REVERT: A 653 GLU cc_start: 0.7755 (pt0) cc_final: 0.7041 (pm20) REVERT: A 758 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7828 (pm20) REVERT: A 944 ARG cc_start: 0.7690 (ptp-110) cc_final: 0.7292 (ttm110) REVERT: A 1009 GLU cc_start: 0.8377 (tt0) cc_final: 0.8152 (tt0) REVERT: A 1013 ASP cc_start: 0.7373 (t0) cc_final: 0.7115 (t0) REVERT: A 1052 MET cc_start: 0.8666 (mmm) cc_final: 0.8037 (mmm) REVERT: A 1086 LYS cc_start: 0.7354 (mtmt) cc_final: 0.6979 (mtpm) REVERT: A 1127 GLN cc_start: 0.7699 (mm-40) cc_final: 0.6880 (mp10) REVERT: A 1138 GLU cc_start: 0.8227 (pt0) cc_final: 0.7905 (pt0) REVERT: A 1161 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6638 (mm-30) REVERT: A 1261 LYS cc_start: 0.5864 (mttp) cc_final: 0.4280 (ttmt) REVERT: A 1445 GLU cc_start: 0.8260 (tt0) cc_final: 0.7831 (tp30) REVERT: A 1474 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5577 (pm20) REVERT: A 1486 MET cc_start: 0.6496 (tmm) cc_final: 0.6008 (tmt) REVERT: A 1518 LYS cc_start: 0.5861 (pmtt) cc_final: 0.4631 (mmtt) REVERT: A 1579 VAL cc_start: 0.8272 (m) cc_final: 0.8030 (t) REVERT: A 1635 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8540 (tp) REVERT: A 1707 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7272 (tttt) REVERT: B 325 MET cc_start: 0.1545 (mmp) cc_final: 0.1032 (mmp) REVERT: B 592 ASP cc_start: 0.7348 (m-30) cc_final: 0.7046 (m-30) REVERT: B 680 GLU cc_start: 0.7300 (pt0) cc_final: 0.6994 (pm20) REVERT: B 818 GLN cc_start: 0.6897 (mt0) cc_final: 0.6309 (mp10) REVERT: B 825 LYS cc_start: 0.6431 (pptt) cc_final: 0.6148 (pptt) REVERT: B 831 ILE cc_start: 0.8129 (pt) cc_final: 0.7867 (pp) REVERT: B 980 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7705 (mttt) REVERT: B 1128 ASP cc_start: 0.7633 (m-30) cc_final: 0.7397 (m-30) REVERT: B 1160 ASP cc_start: 0.8124 (m-30) cc_final: 0.7909 (m-30) REVERT: B 1358 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7531 (t) REVERT: B 1363 GLU cc_start: 0.7651 (tt0) cc_final: 0.7430 (mt-10) REVERT: B 1385 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7301 (pp20) REVERT: B 1597 ASP cc_start: 0.7926 (p0) cc_final: 0.7687 (p0) REVERT: B 1617 MET cc_start: 0.4225 (mpt) cc_final: 0.2782 (mpt) REVERT: B 1772 MET cc_start: 0.6907 (pp-130) cc_final: 0.6542 (ppp) REVERT: B 1773 GLU cc_start: 0.5753 (mt-10) cc_final: 0.4752 (mt-10) REVERT: B 1892 LEU cc_start: 0.7199 (mt) cc_final: 0.6780 (mt) REVERT: B 1993 ASP cc_start: 0.5841 (t70) cc_final: 0.5618 (m-30) outliers start: 50 outliers final: 27 residues processed: 322 average time/residue: 0.6949 time to fit residues: 262.7769 Evaluate side-chains 318 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 282 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1201 GLU Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1628 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 980 LYS Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1358 VAL Chi-restraints excluded: chain B residue 1385 GLU Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1754 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 140 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 332 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 274 optimal weight: 0.5980 chunk 222 optimal weight: 4.9990 chunk 336 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN A 904 ASN A1187 GLN ** A1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1619 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.238434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.176557 restraints weight = 58936.948| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.49 r_work: 0.3862 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 27979 Z= 0.145 Angle : 0.657 17.712 37909 Z= 0.334 Chirality : 0.046 0.220 4222 Planarity : 0.005 0.083 4879 Dihedral : 5.134 56.138 3730 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.71 % Favored : 93.06 % Rotamer: Outliers : 1.60 % Allowed : 18.17 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3459 helix: 0.39 (0.14), residues: 1375 sheet: -1.66 (0.24), residues: 454 loop : -1.30 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 470 TYR 0.023 0.001 TYR B1114 PHE 0.026 0.002 PHE A 35 TRP 0.020 0.001 TRP B1137 HIS 0.006 0.001 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00341 (27979) covalent geometry : angle 0.65698 (37909) hydrogen bonds : bond 0.03604 ( 1134) hydrogen bonds : angle 5.05563 ( 3183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16109.95 seconds wall clock time: 273 minutes 10.59 seconds (16390.59 seconds total)