Starting phenix.real_space_refine on Fri Oct 30 04:09:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s8f_10120/10_2026/6s8f_10120.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8f_10120/10_2026/6s8f_10120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6s8f_10120/10_2026/6s8f_10120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8f_10120/10_2026/6s8f_10120.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6s8f_10120/10_2026/6s8f_10120.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s8f_10120/10_2026/6s8f_10120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s8f_10120/10_2026/6s8f_10120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8f_10120/10_2026/6s8f_10120.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 96 5.16 5 C 21440 2.51 5 N 6016 2.21 5 O 6104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.24s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33664 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 16800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2571, 16800 Classifications: {'peptide': 2571} Incomplete info: {'backbone_only': 13, 'truncation_to_alanine': 1276} Link IDs: {'CIS': 3, 'PTRANS': 56, 'TRANS': 2511} Chain breaks: 23 Unresolved non-hydrogen bonds: 3216 Unresolved non-hydrogen angles: 4422 Unresolved non-hydrogen dihedrals: 2087 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'UNK:plan-1': 806, 'GLN:plan1': 17, 'ARG:plan': 17, 'PHE:plan': 15, 'ASN:plan1': 42, 'TYR:plan': 11, 'GLU:plan': 76, 'ASP:plan': 53, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 1750 Chain: "H" Number of atoms: 16800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2571, 16800 Classifications: {'peptide': 2571} Incomplete info: {'backbone_only': 13, 'truncation_to_alanine': 1276} Link IDs: {'CIS': 3, 'PTRANS': 56, 'TRANS': 2511} Chain breaks: 23 Unresolved non-hydrogen bonds: 3216 Unresolved non-hydrogen angles: 4422 Unresolved non-hydrogen dihedrals: 2087 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'UNK:plan-1': 806, 'GLN:plan1': 17, 'ARG:plan': 17, 'PHE:plan': 15, 'ASN:plan1': 42, 'TYR:plan': 11, 'GLU:plan': 76, 'ASP:plan': 53, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 1750 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.61, per 1000 atoms: 0.23 Number of scatterers: 33664 At special positions: 0 Unit cell: (107.415, 213.745, 201.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 6 15.00 Mg 2 11.99 O 6104 8.00 N 6016 7.00 C 21440 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9972 Finding SS restraints... Secondary structure from input PDB file: 286 helices and 4 sheets defined 99.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'F' and resid 9 through 18 removed outlier: 4.297A pdb=" N UNK F 13 " --> pdb=" O UNK F 9 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N UNK F 14 " --> pdb=" O UNK F 10 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N UNK F 15 " --> pdb=" O UNK F 11 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N UNK F 18 " --> pdb=" O UNK F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 35 Processing helix chain 'F' and resid 44 through 70 removed outlier: 4.377A pdb=" N UNK F 48 " --> pdb=" O UNK F 44 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N UNK F 70 " --> pdb=" O UNK F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 97 removed outlier: 3.971A pdb=" N UNK F 80 " --> pdb=" O UNK F 76 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N UNK F 88 " --> pdb=" O UNK F 84 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK F 89 " --> pdb=" O UNK F 85 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N UNK F 97 " --> pdb=" O UNK F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 117 Processing helix chain 'F' and resid 131 through 140 removed outlier: 3.846A pdb=" N UNK F 140 " --> pdb=" O UNK F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 removed outlier: 3.669A pdb=" N UNK F 146 " --> pdb=" O UNK F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 172 removed outlier: 3.885A pdb=" N UNK F 172 " --> pdb=" O UNK F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 removed outlier: 4.251A pdb=" N UNK F 180 " --> pdb=" O UNK F 176 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N UNK F 181 " --> pdb=" O UNK F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 226 Processing helix chain 'F' and resid 230 through 234 removed outlier: 4.261A pdb=" N UNK F 233 " --> pdb=" O UNK F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 250 Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 280 through 293 removed outlier: 3.856A pdb=" N UNK F 284 " --> pdb=" O UNK F 280 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N UNK F 285 " --> pdb=" O UNK F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 310 through 319 Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 334 through 345 removed outlier: 3.571A pdb=" N UNK F 338 " --> pdb=" O UNK F 334 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N UNK F 341 " --> pdb=" O UNK F 337 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N UNK F 344 " --> pdb=" O UNK F 340 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N UNK F 345 " --> pdb=" O UNK F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 377 removed outlier: 3.505A pdb=" N UNK F 356 " --> pdb=" O UNK F 352 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N UNK F 367 " --> pdb=" O UNK F 363 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N UNK F 368 " --> pdb=" O UNK F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 431 Processing helix chain 'F' and resid 446 through 460 removed outlier: 3.570A pdb=" N UNK F 451 " --> pdb=" O UNK F 447 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N UNK F 452 " --> pdb=" O UNK F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 489 removed outlier: 4.467A pdb=" N UNK F 477 " --> pdb=" O UNK F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 513 No H-bonds generated for 'chain 'F' and resid 511 through 513' Processing helix chain 'F' and resid 514 through 532 removed outlier: 4.190A pdb=" N UNK F 519 " --> pdb=" O UNK F 515 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N UNK F 520 " --> pdb=" O UNK F 516 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N UNK F 529 " --> pdb=" O UNK F 525 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N UNK F 530 " --> pdb=" O UNK F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 568 Processing helix chain 'F' and resid 569 through 573 removed outlier: 4.356A pdb=" N UNK F 573 " --> pdb=" O UNK F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 590 removed outlier: 4.475A pdb=" N UNK F 585 " --> pdb=" O UNK F 581 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N UNK F 586 " --> pdb=" O UNK F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 608 Processing helix chain 'F' and resid 612 through 621 Processing helix chain 'F' and resid 627 through 639 Processing helix chain 'F' and resid 647 through 657 removed outlier: 3.865A pdb=" N UNK F 651 " --> pdb=" O UNK F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 678 removed outlier: 3.926A pdb=" N UNK F 670 " --> pdb=" O UNK F 666 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N UNK F 671 " --> pdb=" O UNK F 667 " (cutoff:3.500A) Processing helix chain 'F' and resid 682 through 686 Processing helix chain 'F' and resid 686 through 695 removed outlier: 3.820A pdb=" N UNK F 695 " --> pdb=" O UNK F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 712 through 719 Processing helix chain 'F' and resid 747 through 760 removed outlier: 4.290A pdb=" N UNK F 753 " --> pdb=" O UNK F 749 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N UNK F 759 " --> pdb=" O UNK F 755 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N UNK F 760 " --> pdb=" O UNK F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 772 through 789 removed outlier: 3.781A pdb=" N UNK F 783 " --> pdb=" O UNK F 779 " (cutoff:3.500A) Processing helix chain 'F' and resid 798 through 809 removed outlier: 4.070A pdb=" N UNK F 802 " --> pdb=" O UNK F 798 " (cutoff:3.500A) Processing helix chain 'F' and resid 821 through 834 removed outlier: 3.604A pdb=" N UNK F 834 " --> pdb=" O UNK F 830 " (cutoff:3.500A) Processing helix chain 'F' and resid 839 through 850 Processing helix chain 'F' and resid 861 through 867 Processing helix chain 'F' and resid 883 through 899 removed outlier: 3.928A pdb=" N UNK F 894 " --> pdb=" O UNK F 890 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N UNK F 895 " --> pdb=" O UNK F 891 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N UNK F 896 " --> pdb=" O UNK F 892 " (cutoff:3.500A) Processing helix chain 'F' and resid 903 through 918 removed outlier: 4.707A pdb=" N UNK F 909 " --> pdb=" O UNK F 905 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N UNK F 910 " --> pdb=" O UNK F 906 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N UNK F 911 " --> pdb=" O UNK F 907 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N UNK F 912 " --> pdb=" O UNK F 908 " (cutoff:3.500A) Processing helix chain 'F' and resid 920 through 925 removed outlier: 3.502A pdb=" N UNK F 925 " --> pdb=" O UNK F 921 " (cutoff:3.500A) Processing helix chain 'F' and resid 926 through 943 removed outlier: 4.395A pdb=" N UNK F 930 " --> pdb=" O UNK F 926 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N UNK F 931 " --> pdb=" O UNK F 927 " (cutoff:3.500A) Processing helix chain 'F' and resid 948 through 964 Processing helix chain 'F' and resid 971 through 979 Processing helix chain 'F' and resid 982 through 990 removed outlier: 4.326A pdb=" N LEU F 988 " --> pdb=" O CYS F 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 993 through 1001 removed outlier: 3.601A pdb=" N ASN F 998 " --> pdb=" O ILE F 994 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER F 999 " --> pdb=" O ASN F 995 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER F1001 " --> pdb=" O MET F 997 " (cutoff:3.500A) Processing helix chain 'F' and resid 1002 through 1016 removed outlier: 3.889A pdb=" N GLN F1006 " --> pdb=" O SER F1002 " (cutoff:3.500A) Processing helix chain 'F' and resid 1024 through 1033 removed outlier: 3.535A pdb=" N GLN F1028 " --> pdb=" O GLY F1024 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F1030 " --> pdb=" O PRO F1026 " (cutoff:3.500A) Processing helix chain 'F' and resid 1037 through 1047 removed outlier: 3.555A pdb=" N VAL F1046 " --> pdb=" O MET F1042 " (cutoff:3.500A) Processing helix chain 'F' and resid 1056 through 1072 removed outlier: 4.310A pdb=" N THR F1060 " --> pdb=" O GLU F1056 " (cutoff:3.500A) Processing helix chain 'F' and resid 1085 through 1090 Processing helix chain 'F' and resid 1133 through 1141 removed outlier: 3.638A pdb=" N SER F1139 " --> pdb=" O PHE F1135 " (cutoff:3.500A) Processing helix chain 'F' and resid 1152 through 1160 Processing helix chain 'F' and resid 1164 through 1171 Processing helix chain 'F' and resid 1171 through 1179 removed outlier: 3.540A pdb=" N CYS F1175 " --> pdb=" O SER F1171 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE F1176 " --> pdb=" O TYR F1172 " (cutoff:3.500A) Proline residue: F1177 - end of helix No H-bonds generated for 'chain 'F' and resid 1171 through 1179' Processing helix chain 'F' and resid 1200 through 1208 Processing helix chain 'F' and resid 1208 through 1219 Processing helix chain 'F' and resid 1226 through 1236 Processing helix chain 'F' and resid 1244 through 1251 Processing helix chain 'F' and resid 1267 through 1275 removed outlier: 4.117A pdb=" N GLN F1271 " --> pdb=" O ALA F1267 " (cutoff:3.500A) Processing helix chain 'F' and resid 1280 through 1298 Processing helix chain 'F' and resid 1300 through 1318 removed outlier: 3.595A pdb=" N LYS F1304 " --> pdb=" O THR F1300 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS F1312 " --> pdb=" O ALA F1308 " (cutoff:3.500A) Processing helix chain 'F' and resid 1324 through 1334 removed outlier: 3.842A pdb=" N ARG F1334 " --> pdb=" O PHE F1330 " (cutoff:3.500A) Processing helix chain 'F' and resid 1335 through 1342 removed outlier: 3.544A pdb=" N PHE F1338 " --> pdb=" O LEU F1335 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F1339 " --> pdb=" O SER F1336 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE F1340 " --> pdb=" O LYS F1337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP F1341 " --> pdb=" O PHE F1338 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F1342 " --> pdb=" O LEU F1339 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1335 through 1342' Processing helix chain 'F' and resid 1344 through 1362 removed outlier: 3.991A pdb=" N ILE F1351 " --> pdb=" O GLU F1347 " (cutoff:3.500A) Processing helix chain 'F' and resid 1366 through 1368 No H-bonds generated for 'chain 'F' and resid 1366 through 1368' Processing helix chain 'F' and resid 1369 through 1383 removed outlier: 4.163A pdb=" N LEU F1373 " --> pdb=" O SER F1369 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS F1376 " --> pdb=" O ASN F1372 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE F1378 " --> pdb=" O PHE F1374 " (cutoff:3.500A) Processing helix chain 'F' and resid 1388 through 1398 removed outlier: 3.547A pdb=" N LEU F1397 " --> pdb=" O GLN F1393 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU F1398 " --> pdb=" O ALA F1394 " (cutoff:3.500A) Processing helix chain 'F' and resid 1405 through 1417 removed outlier: 3.721A pdb=" N PHE F1417 " --> pdb=" O LEU F1413 " (cutoff:3.500A) Processing helix chain 'F' and resid 1422 through 1428 removed outlier: 4.005A pdb=" N ILE F1425 " --> pdb=" O GLN F1422 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR F1426 " --> pdb=" O ASP F1423 " (cutoff:3.500A) Processing helix chain 'F' and resid 1438 through 1450 removed outlier: 3.811A pdb=" N VAL F1442 " --> pdb=" O GLY F1438 " (cutoff:3.500A) Processing helix chain 'F' and resid 1456 through 1461 removed outlier: 4.190A pdb=" N GLY F1461 " --> pdb=" O ALA F1457 " (cutoff:3.500A) Processing helix chain 'F' and resid 1484 through 1506 removed outlier: 4.791A pdb=" N ARG F1495 " --> pdb=" O ALA F1491 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG F1496 " --> pdb=" O ALA F1492 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F1503 " --> pdb=" O GLN F1499 " (cutoff:3.500A) Processing helix chain 'F' and resid 1513 through 1524 removed outlier: 4.240A pdb=" N LYS F1517 " --> pdb=" O GLU F1513 " (cutoff:3.500A) Processing helix chain 'F' and resid 1529 through 1541 removed outlier: 3.626A pdb=" N TYR F1533 " --> pdb=" O PRO F1529 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN F1534 " --> pdb=" O HIS F1530 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS F1541 " --> pdb=" O SER F1537 " (cutoff:3.500A) Processing helix chain 'F' and resid 1542 through 1548 removed outlier: 3.829A pdb=" N ASP F1547 " --> pdb=" O GLU F1544 " (cutoff:3.500A) Processing helix chain 'F' and resid 1550 through 1565 Processing helix chain 'F' and resid 1576 through 1581 Processing helix chain 'F' and resid 1589 through 1597 Processing helix chain 'F' and resid 1611 through 1615 removed outlier: 3.766A pdb=" N THR F1615 " --> pdb=" O ILE F1612 " (cutoff:3.500A) Processing helix chain 'F' and resid 1622 through 1639 removed outlier: 3.658A pdb=" N GLN F1637 " --> pdb=" O SER F1633 " (cutoff:3.500A) Processing helix chain 'F' and resid 1643 through 1647 removed outlier: 3.784A pdb=" N VAL F1646 " --> pdb=" O PRO F1643 " (cutoff:3.500A) Processing helix chain 'F' and resid 1648 through 1654 removed outlier: 3.711A pdb=" N LYS F1653 " --> pdb=" O TYR F1649 " (cutoff:3.500A) Processing helix chain 'F' and resid 1657 through 1673 removed outlier: 4.179A pdb=" N LEU F1661 " --> pdb=" O ALA F1657 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR F1664 " --> pdb=" O GLU F1660 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP F1665 " --> pdb=" O LEU F1661 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR F1673 " --> pdb=" O LEU F1669 " (cutoff:3.500A) Processing helix chain 'F' and resid 1674 through 1687 removed outlier: 4.299A pdb=" N ASN F1680 " --> pdb=" O LYS F1676 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG F1684 " --> pdb=" O ASN F1680 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE F1685 " --> pdb=" O TRP F1681 " (cutoff:3.500A) Processing helix chain 'F' and resid 1688 through 1689 No H-bonds generated for 'chain 'F' and resid 1688 through 1689' Processing helix chain 'F' and resid 1690 through 1694 removed outlier: 3.501A pdb=" N HIS F1694 " --> pdb=" O MET F1691 " (cutoff:3.500A) Processing helix chain 'F' and resid 1697 through 1718 removed outlier: 3.602A pdb=" N LYS F1701 " --> pdb=" O ASP F1697 " (cutoff:3.500A) Processing helix chain 'F' and resid 1720 through 1728 removed outlier: 3.747A pdb=" N ARG F1725 " --> pdb=" O ARG F1721 " (cutoff:3.500A) Processing helix chain 'F' and resid 1731 through 1742 removed outlier: 3.612A pdb=" N ILE F1735 " --> pdb=" O ASP F1731 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU F1740 " --> pdb=" O CYS F1736 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS F1741 " --> pdb=" O GLN F1737 " (cutoff:3.500A) Processing helix chain 'F' and resid 1745 through 1756 Processing helix chain 'F' and resid 1759 through 1763 Processing helix chain 'F' and resid 1764 through 1774 removed outlier: 4.142A pdb=" N LYS F1770 " --> pdb=" O ASN F1766 " (cutoff:3.500A) Processing helix chain 'F' and resid 1780 through 1784 removed outlier: 4.335A pdb=" N GLY F1783 " --> pdb=" O PHE F1780 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F1784 " --> pdb=" O LEU F1781 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1780 through 1784' Processing helix chain 'F' and resid 1789 through 1800 removed outlier: 3.723A pdb=" N VAL F1793 " --> pdb=" O SER F1789 " (cutoff:3.500A) Processing helix chain 'F' and resid 1803 through 1818 Processing helix chain 'F' and resid 1819 through 1822 removed outlier: 3.562A pdb=" N SER F1822 " --> pdb=" O TYR F1819 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1819 through 1822' Processing helix chain 'F' and resid 1826 through 1838 removed outlier: 3.796A pdb=" N LEU F1830 " --> pdb=" O GLU F1826 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS F1832 " --> pdb=" O GLU F1828 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA F1833 " --> pdb=" O SER F1829 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP F1836 " --> pdb=" O LYS F1832 " (cutoff:3.500A) Processing helix chain 'F' and resid 1839 through 1847 Processing helix chain 'F' and resid 1855 through 1864 removed outlier: 4.034A pdb=" N TRP F1859 " --> pdb=" O ASP F1855 " (cutoff:3.500A) Processing helix chain 'F' and resid 1877 through 1887 Processing helix chain 'F' and resid 1894 through 1909 Processing helix chain 'F' and resid 1915 through 1934 removed outlier: 3.723A pdb=" N TRP F1919 " --> pdb=" O SER F1915 " (cutoff:3.500A) Processing helix chain 'F' and resid 1941 through 1958 removed outlier: 3.845A pdb=" N THR F1945 " --> pdb=" O SER F1941 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU F1955 " --> pdb=" O LYS F1951 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU F1957 " --> pdb=" O ASP F1953 " (cutoff:3.500A) Processing helix chain 'F' and resid 1961 through 1984 removed outlier: 3.851A pdb=" N HIS F1965 " --> pdb=" O ASP F1961 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR F1967 " --> pdb=" O TYR F1963 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR F1968 " --> pdb=" O ASP F1964 " (cutoff:3.500A) Processing helix chain 'F' and resid 1987 through 2012 removed outlier: 3.663A pdb=" N LYS F1992 " --> pdb=" O VAL F1988 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR F1993 " --> pdb=" O LYS F1989 " (cutoff:3.500A) Processing helix chain 'F' and resid 2014 through 2032 removed outlier: 3.699A pdb=" N ARG F2020 " --> pdb=" O GLN F2016 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN F2021 " --> pdb=" O ASP F2017 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN F2031 " --> pdb=" O LYS F2027 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE F2032 " --> pdb=" O THR F2028 " (cutoff:3.500A) Processing helix chain 'F' and resid 2038 through 2060 Processing helix chain 'F' and resid 2064 through 2080 Processing helix chain 'F' and resid 2081 through 2085 removed outlier: 3.740A pdb=" N SER F2084 " --> pdb=" O ILE F2081 " (cutoff:3.500A) Processing helix chain 'F' and resid 2107 through 2112 removed outlier: 3.788A pdb=" N GLU F2111 " --> pdb=" O LYS F2107 " (cutoff:3.500A) Processing helix chain 'F' and resid 2116 through 2124 Processing helix chain 'F' and resid 2137 through 2159 removed outlier: 3.906A pdb=" N VAL F2141 " --> pdb=" O SER F2137 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE F2142 " --> pdb=" O CYS F2138 " (cutoff:3.500A) Processing helix chain 'F' and resid 2161 through 2180 removed outlier: 3.575A pdb=" N HIS F2167 " --> pdb=" O GLU F2163 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU F2180 " --> pdb=" O LEU F2176 " (cutoff:3.500A) Processing helix chain 'F' and resid 2200 through 2237 removed outlier: 3.535A pdb=" N VAL F2237 " --> pdb=" O LEU F2233 " (cutoff:3.500A) Processing helix chain 'F' and resid 2244 through 2257 removed outlier: 3.938A pdb=" N ASP F2248 " --> pdb=" O ASN F2244 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS F2249 " --> pdb=" O ASP F2245 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY F2252 " --> pdb=" O ASP F2248 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE F2255 " --> pdb=" O CYS F2251 " (cutoff:3.500A) Processing helix chain 'F' and resid 2260 through 2266 Processing helix chain 'F' and resid 2266 through 2271 removed outlier: 4.121A pdb=" N GLU F2270 " --> pdb=" O LEU F2266 " (cutoff:3.500A) Processing helix chain 'F' and resid 2275 through 2280 removed outlier: 3.560A pdb=" N LEU F2280 " --> pdb=" O TRP F2277 " (cutoff:3.500A) Processing helix chain 'F' and resid 2298 through 2312 removed outlier: 3.799A pdb=" N GLN F2302 " --> pdb=" O GLN F2298 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG F2307 " --> pdb=" O LEU F2303 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR F2310 " --> pdb=" O LYS F2306 " (cutoff:3.500A) Processing helix chain 'F' and resid 2316 through 2325 Processing helix chain 'F' and resid 2333 through 2352 removed outlier: 3.580A pdb=" N LYS F2339 " --> pdb=" O ASN F2335 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY F2352 " --> pdb=" O LEU F2348 " (cutoff:3.500A) Processing helix chain 'F' and resid 2357 through 2362 removed outlier: 3.788A pdb=" N LYS F2361 " --> pdb=" O ALA F2357 " (cutoff:3.500A) Processing helix chain 'F' and resid 2362 through 2377 removed outlier: 3.638A pdb=" N ALA F2377 " --> pdb=" O SER F2373 " (cutoff:3.500A) Processing helix chain 'F' and resid 2397 through 2402 Processing helix chain 'F' and resid 2472 through 2489 Processing helix chain 'F' and resid 2491 through 2496 Processing helix chain 'F' and resid 2525 through 2533 Processing helix chain 'F' and resid 2539 through 2550 removed outlier: 3.577A pdb=" N ARG F2544 " --> pdb=" O PHE F2540 " (cutoff:3.500A) Processing helix chain 'F' and resid 2554 through 2569 removed outlier: 4.346A pdb=" N GLU F2568 " --> pdb=" O LYS F2564 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE F2569 " --> pdb=" O ILE F2565 " (cutoff:3.500A) Processing helix chain 'F' and resid 2574 through 2581 removed outlier: 3.551A pdb=" N PHE F2578 " --> pdb=" O ARG F2574 " (cutoff:3.500A) Processing helix chain 'F' and resid 2583 through 2608 removed outlier: 4.459A pdb=" N GLU F2589 " --> pdb=" O LEU F2585 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS F2596 " --> pdb=" O LYS F2592 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F2604 " --> pdb=" O ALA F2600 " (cutoff:3.500A) Processing helix chain 'F' and resid 2637 through 2641 Processing helix chain 'F' and resid 2653 through 2658 Processing helix chain 'F' and resid 2668 through 2683 removed outlier: 3.761A pdb=" N VAL F2679 " --> pdb=" O ARG F2675 " (cutoff:3.500A) Processing helix chain 'F' and resid 2684 through 2692 removed outlier: 3.686A pdb=" N MET F2688 " --> pdb=" O TYR F2684 " (cutoff:3.500A) Processing helix chain 'F' and resid 2707 through 2717 Processing helix chain 'F' and resid 2736 through 2754 removed outlier: 3.699A pdb=" N MET F2753 " --> pdb=" O GLU F2749 " (cutoff:3.500A) Processing helix chain 'F' and resid 2758 through 2771 removed outlier: 3.918A pdb=" N GLN F2764 " --> pdb=" O GLU F2760 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F2766 " --> pdb=" O SER F2762 " (cutoff:3.500A) Processing helix chain 'F' and resid 2772 through 2777 Processing helix chain 'H' and resid 9 through 18 removed outlier: 4.377A pdb=" N UNK H 13 " --> pdb=" O UNK H 9 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N UNK H 14 " --> pdb=" O UNK H 10 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N UNK H 15 " --> pdb=" O UNK H 11 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N UNK H 18 " --> pdb=" O UNK H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 35 Processing helix chain 'H' and resid 44 through 70 removed outlier: 4.376A pdb=" N UNK H 48 " --> pdb=" O UNK H 44 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N UNK H 70 " --> pdb=" O UNK H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 97 removed outlier: 3.959A pdb=" N UNK H 80 " --> pdb=" O UNK H 76 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N UNK H 88 " --> pdb=" O UNK H 84 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNK H 89 " --> pdb=" O UNK H 85 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N UNK H 97 " --> pdb=" O UNK H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 117 Processing helix chain 'H' and resid 131 through 140 removed outlier: 3.924A pdb=" N UNK H 140 " --> pdb=" O UNK H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 147 removed outlier: 3.671A pdb=" N UNK H 146 " --> pdb=" O UNK H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 172 removed outlier: 3.894A pdb=" N UNK H 172 " --> pdb=" O UNK H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 193 removed outlier: 3.765A pdb=" N UNK H 178 " --> pdb=" O UNK H 174 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N UNK H 180 " --> pdb=" O UNK H 176 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N UNK H 181 " --> pdb=" O UNK H 177 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N UNK H 183 " --> pdb=" O UNK H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 226 Processing helix chain 'H' and resid 230 through 234 removed outlier: 4.284A pdb=" N UNK H 233 " --> pdb=" O UNK H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 250 Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 280 through 293 removed outlier: 3.847A pdb=" N UNK H 284 " --> pdb=" O UNK H 280 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK H 285 " --> pdb=" O UNK H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 304 Processing helix chain 'H' and resid 310 through 319 Processing helix chain 'H' and resid 322 through 332 Processing helix chain 'H' and resid 334 through 345 removed outlier: 3.551A pdb=" N UNK H 338 " --> pdb=" O UNK H 334 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N UNK H 341 " --> pdb=" O UNK H 337 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N UNK H 344 " --> pdb=" O UNK H 340 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N UNK H 345 " --> pdb=" O UNK H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 352 through 377 removed outlier: 4.135A pdb=" N UNK H 367 " --> pdb=" O UNK H 363 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N UNK H 368 " --> pdb=" O UNK H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 424 through 431 Processing helix chain 'H' and resid 446 through 460 removed outlier: 3.580A pdb=" N UNK H 451 " --> pdb=" O UNK H 447 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N UNK H 452 " --> pdb=" O UNK H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 473 through 489 removed outlier: 4.479A pdb=" N UNK H 477 " --> pdb=" O UNK H 473 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 513 No H-bonds generated for 'chain 'H' and resid 511 through 513' Processing helix chain 'H' and resid 514 through 532 removed outlier: 4.198A pdb=" N UNK H 519 " --> pdb=" O UNK H 515 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N UNK H 520 " --> pdb=" O UNK H 516 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N UNK H 529 " --> pdb=" O UNK H 525 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N UNK H 530 " --> pdb=" O UNK H 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 560 through 568 Processing helix chain 'H' and resid 569 through 573 removed outlier: 4.358A pdb=" N UNK H 573 " --> pdb=" O UNK H 570 " (cutoff:3.500A) Processing helix chain 'H' and resid 580 through 590 removed outlier: 4.492A pdb=" N UNK H 585 " --> pdb=" O UNK H 581 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N UNK H 586 " --> pdb=" O UNK H 582 " (cutoff:3.500A) Processing helix chain 'H' and resid 603 through 608 Processing helix chain 'H' and resid 612 through 621 Processing helix chain 'H' and resid 627 through 639 Processing helix chain 'H' and resid 647 through 657 removed outlier: 3.888A pdb=" N UNK H 651 " --> pdb=" O UNK H 647 " (cutoff:3.500A) Processing helix chain 'H' and resid 666 through 678 removed outlier: 3.912A pdb=" N UNK H 670 " --> pdb=" O UNK H 666 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N UNK H 671 " --> pdb=" O UNK H 667 " (cutoff:3.500A) Processing helix chain 'H' and resid 682 through 686 Processing helix chain 'H' and resid 686 through 695 removed outlier: 3.840A pdb=" N UNK H 695 " --> pdb=" O UNK H 691 " (cutoff:3.500A) Processing helix chain 'H' and resid 712 through 719 Processing helix chain 'H' and resid 747 through 760 removed outlier: 4.286A pdb=" N UNK H 753 " --> pdb=" O UNK H 749 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N UNK H 759 " --> pdb=" O UNK H 755 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N UNK H 760 " --> pdb=" O UNK H 756 " (cutoff:3.500A) Processing helix chain 'H' and resid 772 through 789 removed outlier: 3.780A pdb=" N UNK H 783 " --> pdb=" O UNK H 779 " (cutoff:3.500A) Processing helix chain 'H' and resid 798 through 809 removed outlier: 4.063A pdb=" N UNK H 802 " --> pdb=" O UNK H 798 " (cutoff:3.500A) Processing helix chain 'H' and resid 821 through 834 removed outlier: 3.586A pdb=" N UNK H 834 " --> pdb=" O UNK H 830 " (cutoff:3.500A) Processing helix chain 'H' and resid 839 through 850 Processing helix chain 'H' and resid 861 through 867 Processing helix chain 'H' and resid 883 through 899 removed outlier: 3.917A pdb=" N UNK H 894 " --> pdb=" O UNK H 890 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N UNK H 895 " --> pdb=" O UNK H 891 " (cutoff:3.500A) Processing helix chain 'H' and resid 903 through 918 removed outlier: 4.673A pdb=" N UNK H 909 " --> pdb=" O UNK H 905 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N UNK H 910 " --> pdb=" O UNK H 906 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N UNK H 911 " --> pdb=" O UNK H 907 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N UNK H 912 " --> pdb=" O UNK H 908 " (cutoff:3.500A) Processing helix chain 'H' and resid 920 through 925 Processing helix chain 'H' and resid 926 through 943 removed outlier: 4.389A pdb=" N UNK H 930 " --> pdb=" O UNK H 926 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N UNK H 931 " --> pdb=" O UNK H 927 " (cutoff:3.500A) Processing helix chain 'H' and resid 948 through 964 Processing helix chain 'H' and resid 971 through 979 Processing helix chain 'H' and resid 982 through 990 removed outlier: 4.325A pdb=" N LEU H 988 " --> pdb=" O CYS H 984 " (cutoff:3.500A) Processing helix chain 'H' and resid 993 through 1001 removed outlier: 3.608A pdb=" N ASN H 998 " --> pdb=" O ILE H 994 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER H 999 " --> pdb=" O ASN H 995 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER H1001 " --> pdb=" O MET H 997 " (cutoff:3.500A) Processing helix chain 'H' and resid 1002 through 1016 removed outlier: 3.896A pdb=" N GLN H1006 " --> pdb=" O SER H1002 " (cutoff:3.500A) Processing helix chain 'H' and resid 1024 through 1033 removed outlier: 3.551A pdb=" N GLN H1028 " --> pdb=" O GLY H1024 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE H1030 " --> pdb=" O PRO H1026 " (cutoff:3.500A) Processing helix chain 'H' and resid 1037 through 1047 removed outlier: 3.557A pdb=" N VAL H1046 " --> pdb=" O MET H1042 " (cutoff:3.500A) Processing helix chain 'H' and resid 1056 through 1072 removed outlier: 4.304A pdb=" N THR H1060 " --> pdb=" O GLU H1056 " (cutoff:3.500A) Processing helix chain 'H' and resid 1085 through 1090 Processing helix chain 'H' and resid 1133 through 1141 removed outlier: 3.636A pdb=" N SER H1139 " --> pdb=" O PHE H1135 " (cutoff:3.500A) Processing helix chain 'H' and resid 1152 through 1160 Processing helix chain 'H' and resid 1164 through 1171 Processing helix chain 'H' and resid 1171 through 1179 removed outlier: 3.545A pdb=" N CYS H1175 " --> pdb=" O SER H1171 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE H1176 " --> pdb=" O TYR H1172 " (cutoff:3.500A) Proline residue: H1177 - end of helix No H-bonds generated for 'chain 'H' and resid 1171 through 1179' Processing helix chain 'H' and resid 1200 through 1208 Processing helix chain 'H' and resid 1208 through 1219 Processing helix chain 'H' and resid 1226 through 1236 Processing helix chain 'H' and resid 1244 through 1251 Processing helix chain 'H' and resid 1267 through 1275 removed outlier: 4.096A pdb=" N GLN H1271 " --> pdb=" O ALA H1267 " (cutoff:3.500A) Processing helix chain 'H' and resid 1280 through 1298 Processing helix chain 'H' and resid 1300 through 1318 removed outlier: 3.594A pdb=" N LYS H1304 " --> pdb=" O THR H1300 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS H1312 " --> pdb=" O ALA H1308 " (cutoff:3.500A) Processing helix chain 'H' and resid 1324 through 1334 removed outlier: 3.835A pdb=" N ARG H1334 " --> pdb=" O PHE H1330 " (cutoff:3.500A) Processing helix chain 'H' and resid 1335 through 1342 removed outlier: 3.535A pdb=" N PHE H1338 " --> pdb=" O LEU H1335 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU H1339 " --> pdb=" O SER H1336 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE H1340 " --> pdb=" O LYS H1337 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP H1341 " --> pdb=" O PHE H1338 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR H1342 " --> pdb=" O LEU H1339 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1335 through 1342' Processing helix chain 'H' and resid 1344 through 1362 removed outlier: 3.987A pdb=" N ILE H1351 " --> pdb=" O GLU H1347 " (cutoff:3.500A) Processing helix chain 'H' and resid 1366 through 1368 No H-bonds generated for 'chain 'H' and resid 1366 through 1368' Processing helix chain 'H' and resid 1369 through 1383 removed outlier: 4.161A pdb=" N LEU H1373 " --> pdb=" O SER H1369 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS H1376 " --> pdb=" O ASN H1372 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE H1378 " --> pdb=" O PHE H1374 " (cutoff:3.500A) Processing helix chain 'H' and resid 1388 through 1398 removed outlier: 3.569A pdb=" N LEU H1397 " --> pdb=" O GLN H1393 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU H1398 " --> pdb=" O ALA H1394 " (cutoff:3.500A) Processing helix chain 'H' and resid 1405 through 1417 removed outlier: 3.736A pdb=" N PHE H1417 " --> pdb=" O LEU H1413 " (cutoff:3.500A) Processing helix chain 'H' and resid 1422 through 1428 removed outlier: 4.003A pdb=" N ILE H1425 " --> pdb=" O GLN H1422 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR H1426 " --> pdb=" O ASP H1423 " (cutoff:3.500A) Processing helix chain 'H' and resid 1438 through 1450 removed outlier: 3.814A pdb=" N VAL H1442 " --> pdb=" O GLY H1438 " (cutoff:3.500A) Processing helix chain 'H' and resid 1456 through 1461 removed outlier: 4.178A pdb=" N GLY H1461 " --> pdb=" O ALA H1457 " (cutoff:3.500A) Processing helix chain 'H' and resid 1484 through 1506 removed outlier: 4.790A pdb=" N ARG H1495 " --> pdb=" O ALA H1491 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG H1496 " --> pdb=" O ALA H1492 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN H1503 " --> pdb=" O GLN H1499 " (cutoff:3.500A) Processing helix chain 'H' and resid 1513 through 1524 removed outlier: 4.238A pdb=" N LYS H1517 " --> pdb=" O GLU H1513 " (cutoff:3.500A) Processing helix chain 'H' and resid 1529 through 1541 removed outlier: 3.599A pdb=" N TYR H1533 " --> pdb=" O PRO H1529 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN H1534 " --> pdb=" O HIS H1530 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS H1541 " --> pdb=" O SER H1537 " (cutoff:3.500A) Processing helix chain 'H' and resid 1542 through 1548 removed outlier: 3.825A pdb=" N ASP H1547 " --> pdb=" O GLU H1544 " (cutoff:3.500A) Processing helix chain 'H' and resid 1550 through 1565 Processing helix chain 'H' and resid 1576 through 1581 Processing helix chain 'H' and resid 1589 through 1597 Processing helix chain 'H' and resid 1611 through 1615 removed outlier: 3.758A pdb=" N THR H1615 " --> pdb=" O ILE H1612 " (cutoff:3.500A) Processing helix chain 'H' and resid 1622 through 1639 removed outlier: 3.645A pdb=" N GLN H1637 " --> pdb=" O SER H1633 " (cutoff:3.500A) Processing helix chain 'H' and resid 1643 through 1647 removed outlier: 3.773A pdb=" N VAL H1646 " --> pdb=" O PRO H1643 " (cutoff:3.500A) Processing helix chain 'H' and resid 1648 through 1654 removed outlier: 3.702A pdb=" N LYS H1653 " --> pdb=" O TYR H1649 " (cutoff:3.500A) Processing helix chain 'H' and resid 1657 through 1673 removed outlier: 4.180A pdb=" N LEU H1661 " --> pdb=" O ALA H1657 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR H1664 " --> pdb=" O GLU H1660 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP H1665 " --> pdb=" O LEU H1661 " (cutoff:3.500A) Processing helix chain 'H' and resid 1674 through 1687 removed outlier: 4.304A pdb=" N ASN H1680 " --> pdb=" O LYS H1676 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG H1684 " --> pdb=" O ASN H1680 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE H1685 " --> pdb=" O TRP H1681 " (cutoff:3.500A) Processing helix chain 'H' and resid 1688 through 1689 No H-bonds generated for 'chain 'H' and resid 1688 through 1689' Processing helix chain 'H' and resid 1690 through 1694 removed outlier: 3.508A pdb=" N HIS H1694 " --> pdb=" O MET H1691 " (cutoff:3.500A) Processing helix chain 'H' and resid 1697 through 1718 removed outlier: 3.602A pdb=" N LYS H1701 " --> pdb=" O ASP H1697 " (cutoff:3.500A) Processing helix chain 'H' and resid 1720 through 1728 removed outlier: 3.765A pdb=" N ARG H1725 " --> pdb=" O ARG H1721 " (cutoff:3.500A) Processing helix chain 'H' and resid 1731 through 1742 removed outlier: 3.616A pdb=" N ILE H1735 " --> pdb=" O ASP H1731 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU H1740 " --> pdb=" O CYS H1736 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS H1741 " --> pdb=" O GLN H1737 " (cutoff:3.500A) Processing helix chain 'H' and resid 1745 through 1756 Processing helix chain 'H' and resid 1759 through 1763 Processing helix chain 'H' and resid 1764 through 1774 removed outlier: 4.130A pdb=" N LYS H1770 " --> pdb=" O ASN H1766 " (cutoff:3.500A) Processing helix chain 'H' and resid 1780 through 1784 removed outlier: 4.326A pdb=" N GLY H1783 " --> pdb=" O PHE H1780 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU H1784 " --> pdb=" O LEU H1781 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1780 through 1784' Processing helix chain 'H' and resid 1789 through 1800 removed outlier: 3.756A pdb=" N VAL H1793 " --> pdb=" O SER H1789 " (cutoff:3.500A) Processing helix chain 'H' and resid 1803 through 1818 Processing helix chain 'H' and resid 1819 through 1822 removed outlier: 3.559A pdb=" N SER H1822 " --> pdb=" O TYR H1819 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1819 through 1822' Processing helix chain 'H' and resid 1826 through 1838 removed outlier: 3.772A pdb=" N LEU H1830 " --> pdb=" O GLU H1826 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS H1832 " --> pdb=" O GLU H1828 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA H1833 " --> pdb=" O SER H1829 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP H1836 " --> pdb=" O LYS H1832 " (cutoff:3.500A) Processing helix chain 'H' and resid 1839 through 1845 Processing helix chain 'H' and resid 1855 through 1864 removed outlier: 4.035A pdb=" N TRP H1859 " --> pdb=" O ASP H1855 " (cutoff:3.500A) Processing helix chain 'H' and resid 1877 through 1887 Processing helix chain 'H' and resid 1894 through 1909 Processing helix chain 'H' and resid 1915 through 1934 removed outlier: 3.727A pdb=" N TRP H1919 " --> pdb=" O SER H1915 " (cutoff:3.500A) Processing helix chain 'H' and resid 1941 through 1958 removed outlier: 3.836A pdb=" N THR H1945 " --> pdb=" O SER H1941 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU H1955 " --> pdb=" O LYS H1951 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H1957 " --> pdb=" O ASP H1953 " (cutoff:3.500A) Processing helix chain 'H' and resid 1961 through 1984 removed outlier: 3.861A pdb=" N HIS H1965 " --> pdb=" O ASP H1961 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N THR H1967 " --> pdb=" O TYR H1963 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR H1968 " --> pdb=" O ASP H1964 " (cutoff:3.500A) Processing helix chain 'H' and resid 1987 through 2012 removed outlier: 3.655A pdb=" N LYS H1992 " --> pdb=" O VAL H1988 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR H1993 " --> pdb=" O LYS H1989 " (cutoff:3.500A) Processing helix chain 'H' and resid 2014 through 2032 removed outlier: 3.703A pdb=" N ARG H2020 " --> pdb=" O GLN H2016 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN H2021 " --> pdb=" O ASP H2017 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN H2031 " --> pdb=" O LYS H2027 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE H2032 " --> pdb=" O THR H2028 " (cutoff:3.500A) Processing helix chain 'H' and resid 2038 through 2060 Processing helix chain 'H' and resid 2064 through 2080 Processing helix chain 'H' and resid 2081 through 2085 removed outlier: 3.736A pdb=" N SER H2084 " --> pdb=" O ILE H2081 " (cutoff:3.500A) Processing helix chain 'H' and resid 2107 through 2112 removed outlier: 3.784A pdb=" N GLU H2111 " --> pdb=" O LYS H2107 " (cutoff:3.500A) Processing helix chain 'H' and resid 2116 through 2124 Processing helix chain 'H' and resid 2137 through 2159 removed outlier: 3.900A pdb=" N VAL H2141 " --> pdb=" O SER H2137 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE H2142 " --> pdb=" O CYS H2138 " (cutoff:3.500A) Processing helix chain 'H' and resid 2161 through 2180 removed outlier: 3.552A pdb=" N HIS H2167 " --> pdb=" O GLU H2163 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU H2180 " --> pdb=" O LEU H2176 " (cutoff:3.500A) Processing helix chain 'H' and resid 2200 through 2237 removed outlier: 3.537A pdb=" N VAL H2237 " --> pdb=" O LEU H2233 " (cutoff:3.500A) Processing helix chain 'H' and resid 2244 through 2257 removed outlier: 3.937A pdb=" N ASP H2248 " --> pdb=" O ASN H2244 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS H2249 " --> pdb=" O ASP H2245 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLY H2252 " --> pdb=" O ASP H2248 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N PHE H2255 " --> pdb=" O CYS H2251 " (cutoff:3.500A) Processing helix chain 'H' and resid 2260 through 2266 Processing helix chain 'H' and resid 2266 through 2271 removed outlier: 4.086A pdb=" N GLU H2270 " --> pdb=" O LEU H2266 " (cutoff:3.500A) Processing helix chain 'H' and resid 2275 through 2280 removed outlier: 3.560A pdb=" N LEU H2280 " --> pdb=" O TRP H2277 " (cutoff:3.500A) Processing helix chain 'H' and resid 2298 through 2312 removed outlier: 3.798A pdb=" N GLN H2302 " --> pdb=" O GLN H2298 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG H2307 " --> pdb=" O LEU H2303 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR H2310 " --> pdb=" O LYS H2306 " (cutoff:3.500A) Processing helix chain 'H' and resid 2316 through 2325 Processing helix chain 'H' and resid 2333 through 2352 removed outlier: 3.578A pdb=" N LYS H2339 " --> pdb=" O ASN H2335 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY H2352 " --> pdb=" O LEU H2348 " (cutoff:3.500A) Processing helix chain 'H' and resid 2357 through 2362 removed outlier: 3.788A pdb=" N LYS H2361 " --> pdb=" O ALA H2357 " (cutoff:3.500A) Processing helix chain 'H' and resid 2362 through 2377 removed outlier: 3.638A pdb=" N ALA H2377 " --> pdb=" O SER H2373 " (cutoff:3.500A) Processing helix chain 'H' and resid 2397 through 2402 Processing helix chain 'H' and resid 2472 through 2489 Processing helix chain 'H' and resid 2491 through 2496 Processing helix chain 'H' and resid 2525 through 2533 Processing helix chain 'H' and resid 2539 through 2550 removed outlier: 3.577A pdb=" N ARG H2544 " --> pdb=" O PHE H2540 " (cutoff:3.500A) Processing helix chain 'H' and resid 2554 through 2569 removed outlier: 4.345A pdb=" N GLU H2568 " --> pdb=" O LYS H2564 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE H2569 " --> pdb=" O ILE H2565 " (cutoff:3.500A) Processing helix chain 'H' and resid 2574 through 2581 removed outlier: 3.552A pdb=" N PHE H2578 " --> pdb=" O ARG H2574 " (cutoff:3.500A) Processing helix chain 'H' and resid 2583 through 2608 removed outlier: 4.459A pdb=" N GLU H2589 " --> pdb=" O LEU H2585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS H2596 " --> pdb=" O LYS H2592 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL H2604 " --> pdb=" O ALA H2600 " (cutoff:3.500A) Processing helix chain 'H' and resid 2637 through 2641 Processing helix chain 'H' and resid 2653 through 2658 Processing helix chain 'H' and resid 2668 through 2683 removed outlier: 3.761A pdb=" N VAL H2679 " --> pdb=" O ARG H2675 " (cutoff:3.500A) Processing helix chain 'H' and resid 2684 through 2692 removed outlier: 3.686A pdb=" N MET H2688 " --> pdb=" O TYR H2684 " (cutoff:3.500A) Processing helix chain 'H' and resid 2707 through 2717 Processing helix chain 'H' and resid 2736 through 2754 removed outlier: 3.699A pdb=" N MET H2753 " --> pdb=" O GLU H2749 " (cutoff:3.500A) Processing helix chain 'H' and resid 2758 through 2771 removed outlier: 3.918A pdb=" N GLN H2764 " --> pdb=" O GLU H2760 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU H2766 " --> pdb=" O SER H2762 " (cutoff:3.500A) Processing helix chain 'H' and resid 2772 through 2777 Processing sheet with id=AA1, first strand: chain 'F' and resid 2387 through 2389 removed outlier: 6.494A pdb=" N THR F2436 " --> pdb=" O THR F2451 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR F2451 " --> pdb=" O THR F2436 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 2618 through 2619 Processing sheet with id=AA3, first strand: chain 'H' and resid 2387 through 2389 removed outlier: 6.494A pdb=" N THR H2436 " --> pdb=" O THR H2451 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR H2451 " --> pdb=" O THR H2436 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 2618 through 2619 2080 hydrogen bonds defined for protein. 6132 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: 8.18 Time building geometry restraints manager: 3.39 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: 11087 1.34 - 1.46: 5723 1.46 - 1.57: 17194 1.57 - 1.69: 10 1.69 - 1.81: 150 Bond restraints: 34164 Sorted by residual: bond pdb=" O3A ANP H2801 " pdb=" PB ANP H2801 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" O3A ANP F2801 " pdb=" PB ANP F2801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" N3B ANP F2801 " pdb=" PG ANP F2801 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" N3B ANP H2801 " pdb=" PG ANP H2801 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" O5' ANP H2801 " pdb=" PA ANP H2801 " ideal model delta sigma weight residual 1.655 1.573 0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 34159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.89: 46792 8.89 - 17.77: 40 17.77 - 26.66: 2 26.66 - 35.54: 0 35.54 - 44.43: 6 Bond angle restraints: 46840 Sorted by residual: angle pdb=" O ARG F2355 " pdb=" C ARG F2355 " pdb=" N GLY F2356 " ideal model delta sigma weight residual 122.59 78.16 44.43 1.33e+00 5.65e-01 1.12e+03 angle pdb=" O ARG H2355 " pdb=" C ARG H2355 " pdb=" N GLY H2356 " ideal model delta sigma weight residual 122.59 80.90 41.69 1.33e+00 5.65e-01 9.83e+02 angle pdb=" CA ARG F2355 " pdb=" C ARG F2355 " pdb=" N GLY F2356 " ideal model delta sigma weight residual 116.84 159.94 -43.10 1.71e+00 3.42e-01 6.35e+02 angle pdb=" CA ARG H2355 " pdb=" C ARG H2355 " pdb=" N GLY H2356 " ideal model delta sigma weight residual 116.84 156.90 -40.06 1.71e+00 3.42e-01 5.49e+02 angle pdb=" C ARG F2355 " pdb=" N GLY F2356 " pdb=" CA GLY F2356 " ideal model delta sigma weight residual 121.07 161.03 -39.96 1.79e+00 3.12e-01 4.98e+02 ... (remaining 46835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 19000 15.79 - 31.57: 972 31.57 - 47.36: 220 47.36 - 63.15: 22 63.15 - 78.93: 32 Dihedral angle restraints: 20246 sinusoidal: 5050 harmonic: 15196 Sorted by residual: dihedral pdb=" CA LYS F2380 " pdb=" C LYS F2380 " pdb=" N PHE F2381 " pdb=" CA PHE F2381 " ideal model delta harmonic sigma weight residual 180.00 106.16 73.84 0 5.00e+00 4.00e-02 2.18e+02 dihedral pdb=" CA LYS H2380 " pdb=" C LYS H2380 " pdb=" N PHE H2381 " pdb=" CA PHE H2381 " ideal model delta harmonic sigma weight residual 180.00 106.18 73.82 0 5.00e+00 4.00e-02 2.18e+02 dihedral pdb=" CA VAL H1786 " pdb=" C VAL H1786 " pdb=" N PRO H1787 " pdb=" CA PRO H1787 " ideal model delta harmonic sigma weight residual 180.00 -117.62 -62.38 0 5.00e+00 4.00e-02 1.56e+02 ... (remaining 20243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4889 0.073 - 0.147: 847 0.147 - 0.220: 90 0.220 - 0.294: 8 0.294 - 0.367: 10 Chirality restraints: 5844 Sorted by residual: chirality pdb=" CB ILE H2449 " pdb=" CA ILE H2449 " pdb=" CG1 ILE H2449 " pdb=" CG2 ILE H2449 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB ILE F2449 " pdb=" CA ILE F2449 " pdb=" CG1 ILE F2449 " pdb=" CG2 ILE F2449 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE H2644 " pdb=" CA ILE H2644 " pdb=" CG1 ILE H2644 " pdb=" CG2 ILE H2644 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 5841 not shown) Planarity restraints: 6088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H1786 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO H1787 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO H1787 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO H1787 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F1786 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO F1787 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO F1787 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO F1787 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG H2355 " -0.029 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C ARG H2355 " 0.070 2.00e-02 2.50e+03 pdb=" O ARG H2355 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY H2356 " -0.028 2.00e-02 2.50e+03 ... (remaining 6085 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 107 2.47 - 3.08: 22305 3.08 - 3.68: 53249 3.68 - 4.29: 68774 4.29 - 4.90: 107788 Nonbonded interactions: 252223 Sorted by model distance: nonbonded pdb=" NH2 ARG H1717 " pdb=" OD1 ASP H2579 " model vdw 1.859 3.120 nonbonded pdb=" NH2 ARG F1717 " pdb=" OD1 ASP F2579 " model vdw 1.902 3.120 nonbonded pdb=" O2G ANP H2801 " pdb="MG MG H2802 " model vdw 2.100 2.170 nonbonded pdb=" O2G ANP F2801 " pdb="MG MG F2802 " model vdw 2.100 2.170 nonbonded pdb=" O1A ANP F2801 " pdb="MG MG F2802 " model vdw 2.102 2.170 ... (remaining 252218 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: 0.09 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.740 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.007 0.148 34164 Z= 0.340 Angle : 1.263 44.429 46840 Z= 0.681 Chirality : 0.058 0.367 5844 Planarity : 0.007 0.104 6088 Dihedral : 11.676 78.932 10274 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.58 % Favored : 90.30 % Rotamer: Outliers : 0.80 % Allowed : 11.06 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.35 % 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: -4.38 (0.11), residues: 3506 helix: -2.53 (0.08), residues: 2130 sheet: -3.38 (0.57), residues: 66 loop : -3.33 (0.14), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F2613 TYR 0.023 0.002 TYR F1411 PHE 0.042 0.004 PHE H1780 TRP 0.042 0.004 TRP H2108 HIS 0.012 0.003 HIS H1475 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.34 (34164) covalent geometry : angle 1.26332 / 0.68 (46840) hydrogen bonds : bond 0.18297 / 10.20 ( 2080) hydrogen bonds : angle 7.42278 / 3.93 ( 6132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1493 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9242 (tm) REVERT: F 1920 MET cc_start: 0.9230 (mpp) cc_final: 0.8700 (mpp) REVERT: F 2025 MET cc_start: 0.9287 (ttp) cc_final: 0.9058 (tmm) REVERT: F 2233 LEU cc_start: 0.9667 (mt) cc_final: 0.9402 (pp) REVERT: F 2494 LEU cc_start: 0.7873 (pt) cc_final: 0.7633 (pp) REVERT: H 1493 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9249 (tm) REVERT: H 1920 MET cc_start: 0.9210 (mpp) cc_final: 0.8681 (mpp) REVERT: H 2025 MET cc_start: 0.9268 (ttp) cc_final: 0.9039 (tmm) REVERT: H 2233 LEU cc_start: 0.9670 (mt) cc_final: 0.9411 (pp) REVERT: H 2494 LEU cc_start: 0.7997 (pt) cc_final: 0.7722 (pp) outliers start: 18 outliers final: 0 residues processed: 181 average time/residue: 0.1921 time to fit residues: 58.2229 Evaluate side-chains 114 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain H residue 1493 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F1027 GLN F1145 GLN F1157 HIS F1528 GLN F1534 GLN F1707 ASN F1737 GLN ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1977 ASN F1987 ASN F2001 GLN ** F2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2021 ASN F2230 HIS F2234 ASN F2402 GLN F2453 ASN ** F2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2489 GLN F2490 ASN F2521 ASN F2575 ASN ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2629 HIS H1027 GLN H1145 GLN H1157 HIS ** H1260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1528 GLN H1534 GLN H1707 ASN H1737 GLN ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1977 ASN H1987 ASN H2001 GLN ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2021 ASN H2230 HIS H2234 ASN H2402 GLN H2453 ASN ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2490 ASN H2521 ASN H2575 ASN ** H2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2629 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.044539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.032187 restraints weight = 371623.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.032920 restraints weight = 213526.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.033409 restraints weight = 145410.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.033748 restraints weight = 111448.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.033899 restraints weight = 92538.334| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.123 34164 Z= 0.470 Angle : 0.971 16.699 46840 Z= 0.509 Chirality : 0.045 0.235 5844 Planarity : 0.006 0.103 6088 Dihedral : 6.626 72.330 5342 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.87 % Favored : 89.02 % Rotamer: Outliers : 4.12 % Allowed : 11.64 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.35 % 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: -2.38 (0.14), residues: 3506 helix: -0.84 (0.10), residues: 2218 sheet: -2.28 (0.67), residues: 58 loop : -2.82 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F2675 TYR 0.024 0.003 TYR H2268 PHE 0.036 0.003 PHE H1808 TRP 0.024 0.003 TRP F2226 HIS 0.015 0.003 HIS F2533 Details of bonding type rmsd/Z covalent geometry : bond 0.00944 / 0.47 (34164) covalent geometry : angle 0.97133 / 0.51 (46840) hydrogen bonds : bond 0.04654 / 2.55 ( 2080) hydrogen bonds : angle 5.37369 / 2.85 ( 6132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 97 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1920 MET cc_start: 0.9202 (mpp) cc_final: 0.8707 (mpp) REVERT: F 2025 MET cc_start: 0.9534 (ttp) cc_final: 0.9221 (tmm) REVERT: F 2092 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8670 (tt) REVERT: F 2205 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9335 (mt) REVERT: F 2477 MET cc_start: 0.9508 (tpp) cc_final: 0.8916 (tpp) REVERT: F 2532 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9358 (mt) REVERT: H 1757 MET cc_start: 0.8838 (ttm) cc_final: 0.8637 (ttt) REVERT: H 1920 MET cc_start: 0.9204 (mpp) cc_final: 0.8708 (mpp) REVERT: H 2025 MET cc_start: 0.9526 (ttp) cc_final: 0.9243 (tmm) REVERT: H 2092 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8662 (tt) REVERT: H 2205 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9328 (mt) REVERT: H 2477 MET cc_start: 0.9507 (tpp) cc_final: 0.8942 (tpp) outliers start: 93 outliers final: 21 residues processed: 187 average time/residue: 0.1648 time to fit residues: 55.6656 Evaluate side-chains 118 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1259 LEU Chi-restraints excluded: chain F residue 1460 ILE Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1691 MET Chi-restraints excluded: chain F residue 1771 ILE Chi-restraints excluded: chain F residue 1903 LEU Chi-restraints excluded: chain F residue 2052 THR Chi-restraints excluded: chain F residue 2092 LEU Chi-restraints excluded: chain F residue 2114 LEU Chi-restraints excluded: chain F residue 2205 LEU Chi-restraints excluded: chain F residue 2532 LEU Chi-restraints excluded: chain F residue 2573 LEU Chi-restraints excluded: chain F residue 2693 ILE Chi-restraints excluded: chain H residue 1259 LEU Chi-restraints excluded: chain H residue 1460 ILE Chi-restraints excluded: chain H residue 1493 LEU Chi-restraints excluded: chain H residue 1691 MET Chi-restraints excluded: chain H residue 1771 ILE Chi-restraints excluded: chain H residue 1903 LEU Chi-restraints excluded: chain H residue 2052 THR Chi-restraints excluded: chain H residue 2092 LEU Chi-restraints excluded: chain H residue 2114 LEU Chi-restraints excluded: chain H residue 2205 LEU Chi-restraints excluded: chain H residue 2554 SER Chi-restraints excluded: chain H residue 2573 LEU Chi-restraints excluded: chain H residue 2693 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F1525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1798 ASN ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2055 ASN F2483 GLN ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1798 ASN ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2055 ASN H2483 GLN H2489 GLN ** H2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.043561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.031380 restraints weight = 376088.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.032059 restraints weight = 216465.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.032523 restraints weight = 148114.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.032754 restraints weight = 113514.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.033026 restraints weight = 97484.651| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.147 34164 Z= 0.453 Angle : 0.936 15.552 46840 Z= 0.489 Chirality : 0.045 0.259 5844 Planarity : 0.006 0.101 6088 Dihedral : 6.574 68.050 5342 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.95 % Favored : 86.91 % Rotamer: Outliers : 4.96 % Allowed : 14.34 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.29 % 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: -2.39 (0.13), residues: 3506 helix: -0.76 (0.10), residues: 2260 sheet: -2.52 (0.57), residues: 78 loop : -3.07 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H2654 TYR 0.031 0.003 TYR H2268 PHE 0.035 0.003 PHE H1808 TRP 0.025 0.003 TRP H2226 HIS 0.014 0.003 HIS F2614 Details of bonding type rmsd/Z covalent geometry : bond 0.00921 / 0.45 (34164) covalent geometry : angle 0.93641 / 0.49 (46840) hydrogen bonds : bond 0.04514 / 2.47 ( 2080) hydrogen bonds : angle 5.31545 / 2.83 ( 6132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 99 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1212 MET cc_start: 0.9182 (mtt) cc_final: 0.8489 (mmt) REVERT: F 1920 MET cc_start: 0.9270 (mpp) cc_final: 0.8831 (mpp) REVERT: F 2025 MET cc_start: 0.9546 (ttp) cc_final: 0.9125 (tmm) REVERT: F 2092 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8733 (tt) REVERT: F 2464 MET cc_start: 0.8765 (mmp) cc_final: 0.8550 (mmp) REVERT: F 2477 MET cc_start: 0.9423 (tpp) cc_final: 0.9032 (tpp) REVERT: F 2505 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8678 (mtmt) REVERT: H 1920 MET cc_start: 0.9265 (mpp) cc_final: 0.8830 (mpp) REVERT: H 2025 MET cc_start: 0.9517 (ttp) cc_final: 0.9118 (tmm) REVERT: H 2092 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8732 (tt) REVERT: H 2477 MET cc_start: 0.9414 (tpp) cc_final: 0.9025 (tpp) REVERT: H 2505 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8684 (mtmt) REVERT: H 2532 LEU cc_start: 0.9739 (OUTLIER) cc_final: 0.9478 (mt) REVERT: H 2712 HIS cc_start: 0.9125 (m90) cc_final: 0.8889 (m-70) outliers start: 112 outliers final: 43 residues processed: 204 average time/residue: 0.1678 time to fit residues: 61.9363 Evaluate side-chains 144 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1200 THR Chi-restraints excluded: chain F residue 1284 PHE Chi-restraints excluded: chain F residue 1355 LEU Chi-restraints excluded: chain F residue 1460 ILE Chi-restraints excluded: chain F residue 1471 ASN Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1502 VAL Chi-restraints excluded: chain F residue 1691 MET Chi-restraints excluded: chain F residue 1730 LEU Chi-restraints excluded: chain F residue 1771 ILE Chi-restraints excluded: chain F residue 1804 THR Chi-restraints excluded: chain F residue 1903 LEU Chi-restraints excluded: chain F residue 1922 THR Chi-restraints excluded: chain F residue 1966 LYS Chi-restraints excluded: chain F residue 2048 LEU Chi-restraints excluded: chain F residue 2092 LEU Chi-restraints excluded: chain F residue 2105 LEU Chi-restraints excluded: chain F residue 2114 LEU Chi-restraints excluded: chain F residue 2213 VAL Chi-restraints excluded: chain F residue 2505 LYS Chi-restraints excluded: chain F residue 2547 MET Chi-restraints excluded: chain F residue 2554 SER Chi-restraints excluded: chain F residue 2693 ILE Chi-restraints excluded: chain H residue 1200 THR Chi-restraints excluded: chain H residue 1284 PHE Chi-restraints excluded: chain H residue 1355 LEU Chi-restraints excluded: chain H residue 1460 ILE Chi-restraints excluded: chain H residue 1471 ASN Chi-restraints excluded: chain H residue 1493 LEU Chi-restraints excluded: chain H residue 1502 VAL Chi-restraints excluded: chain H residue 1691 MET Chi-restraints excluded: chain H residue 1730 LEU Chi-restraints excluded: chain H residue 1771 ILE Chi-restraints excluded: chain H residue 1804 THR Chi-restraints excluded: chain H residue 1903 LEU Chi-restraints excluded: chain H residue 1922 THR Chi-restraints excluded: chain H residue 1966 LYS Chi-restraints excluded: chain H residue 2048 LEU Chi-restraints excluded: chain H residue 2092 LEU Chi-restraints excluded: chain H residue 2105 LEU Chi-restraints excluded: chain H residue 2213 VAL Chi-restraints excluded: chain H residue 2454 ILE Chi-restraints excluded: chain H residue 2505 LYS Chi-restraints excluded: chain H residue 2529 LEU Chi-restraints excluded: chain H residue 2532 LEU Chi-restraints excluded: chain H residue 2554 SER Chi-restraints excluded: chain H residue 2573 LEU Chi-restraints excluded: chain H residue 2693 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F1343 GLN ** F1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1540 ASN ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2453 ASN ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1343 GLN ** H1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1540 ASN ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2453 ASN ** H2617 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 = 0.3243 r_free = 0.3243 target = 0.043177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.031102 restraints weight = 377069.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.031791 restraints weight = 217143.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.032248 restraints weight = 148351.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.032573 restraints weight = 113234.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.032734 restraints weight = 93769.867| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.116 34164 Z= 0.451 Angle : 0.924 15.721 46840 Z= 0.480 Chirality : 0.045 0.408 5844 Planarity : 0.006 0.104 6088 Dihedral : 6.504 66.351 5342 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.61 % Favored : 86.31 % Rotamer: Outliers : 6.06 % Allowed : 16.02 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.35 % 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: -2.48 (0.13), residues: 3506 helix: -0.83 (0.10), residues: 2272 sheet: -3.51 (0.48), residues: 66 loop : -3.07 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H1972 TYR 0.023 0.002 TYR F2268 PHE 0.028 0.003 PHE H1808 TRP 0.039 0.003 TRP H1805 HIS 0.010 0.002 HIS F2614 Details of bonding type rmsd/Z covalent geometry : bond 0.00919 / 0.45 (34164) covalent geometry : angle 0.92449 / 0.48 (46840) hydrogen bonds : bond 0.04471 / 2.46 ( 2080) hydrogen bonds : angle 5.35474 / 2.85 ( 6132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 96 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1530 HIS cc_start: 0.8659 (OUTLIER) cc_final: 0.8054 (m-70) REVERT: F 1780 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8619 (t80) REVERT: F 1920 MET cc_start: 0.9269 (mpp) cc_final: 0.8828 (mpp) REVERT: F 1946 LEU cc_start: 0.9450 (tt) cc_final: 0.9071 (tt) REVERT: F 2092 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8739 (tt) REVERT: F 2372 MET cc_start: 0.9010 (mmm) cc_final: 0.8653 (mmm) REVERT: F 2477 MET cc_start: 0.9430 (tpp) cc_final: 0.9043 (tpp) REVERT: F 2505 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8771 (mttp) REVERT: F 2712 HIS cc_start: 0.9250 (m90) cc_final: 0.9008 (m-70) REVERT: F 2753 MET cc_start: 0.8480 (mpp) cc_final: 0.8152 (mpp) REVERT: H 1530 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.8051 (m-70) REVERT: H 1780 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8622 (t80) REVERT: H 1920 MET cc_start: 0.9281 (mpp) cc_final: 0.8833 (mpp) REVERT: H 1946 LEU cc_start: 0.9454 (tt) cc_final: 0.9076 (tt) REVERT: H 2092 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8737 (tt) REVERT: H 2205 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9317 (mt) REVERT: H 2372 MET cc_start: 0.8992 (mmm) cc_final: 0.8644 (mmm) REVERT: H 2477 MET cc_start: 0.9439 (tpp) cc_final: 0.9052 (tpp) REVERT: H 2505 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8781 (mtmt) REVERT: H 2532 LEU cc_start: 0.9730 (OUTLIER) cc_final: 0.9472 (tt) REVERT: H 2712 HIS cc_start: 0.9098 (m90) cc_final: 0.8886 (m-70) outliers start: 137 outliers final: 70 residues processed: 227 average time/residue: 0.1721 time to fit residues: 69.7930 Evaluate side-chains 177 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 97 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1192 ILE Chi-restraints excluded: chain F residue 1200 THR Chi-restraints excluded: chain F residue 1259 LEU Chi-restraints excluded: chain F residue 1340 ILE Chi-restraints excluded: chain F residue 1350 THR Chi-restraints excluded: chain F residue 1355 LEU Chi-restraints excluded: chain F residue 1373 LEU Chi-restraints excluded: chain F residue 1460 ILE Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1502 VAL Chi-restraints excluded: chain F residue 1530 HIS Chi-restraints excluded: chain F residue 1612 ILE Chi-restraints excluded: chain F residue 1691 MET Chi-restraints excluded: chain F residue 1730 LEU Chi-restraints excluded: chain F residue 1771 ILE Chi-restraints excluded: chain F residue 1780 PHE Chi-restraints excluded: chain F residue 1804 THR Chi-restraints excluded: chain F residue 1903 LEU Chi-restraints excluded: chain F residue 1922 THR Chi-restraints excluded: chain F residue 1966 LYS Chi-restraints excluded: chain F residue 1999 ILE Chi-restraints excluded: chain F residue 2048 LEU Chi-restraints excluded: chain F residue 2052 THR Chi-restraints excluded: chain F residue 2092 LEU Chi-restraints excluded: chain F residue 2105 LEU Chi-restraints excluded: chain F residue 2114 LEU Chi-restraints excluded: chain F residue 2213 VAL Chi-restraints excluded: chain F residue 2280 LEU Chi-restraints excluded: chain F residue 2284 ASN Chi-restraints excluded: chain F residue 2317 LEU Chi-restraints excluded: chain F residue 2449 ILE Chi-restraints excluded: chain F residue 2451 THR Chi-restraints excluded: chain F residue 2454 ILE Chi-restraints excluded: chain F residue 2505 LYS Chi-restraints excluded: chain F residue 2519 VAL Chi-restraints excluded: chain F residue 2554 SER Chi-restraints excluded: chain F residue 2573 LEU Chi-restraints excluded: chain F residue 2693 ILE Chi-restraints excluded: chain F residue 2763 VAL Chi-restraints excluded: chain H residue 1192 ILE Chi-restraints excluded: chain H residue 1200 THR Chi-restraints excluded: chain H residue 1259 LEU Chi-restraints excluded: chain H residue 1340 ILE Chi-restraints excluded: chain H residue 1350 THR Chi-restraints excluded: chain H residue 1355 LEU Chi-restraints excluded: chain H residue 1373 LEU Chi-restraints excluded: chain H residue 1460 ILE Chi-restraints excluded: chain H residue 1493 LEU Chi-restraints excluded: chain H residue 1502 VAL Chi-restraints excluded: chain H residue 1530 HIS Chi-restraints excluded: chain H residue 1612 ILE Chi-restraints excluded: chain H residue 1691 MET Chi-restraints excluded: chain H residue 1730 LEU Chi-restraints excluded: chain H residue 1771 ILE Chi-restraints excluded: chain H residue 1780 PHE Chi-restraints excluded: chain H residue 1804 THR Chi-restraints excluded: chain H residue 1903 LEU Chi-restraints excluded: chain H residue 1922 THR Chi-restraints excluded: chain H residue 1966 LYS Chi-restraints excluded: chain H residue 1999 ILE Chi-restraints excluded: chain H residue 2048 LEU Chi-restraints excluded: chain H residue 2052 THR Chi-restraints excluded: chain H residue 2092 LEU Chi-restraints excluded: chain H residue 2105 LEU Chi-restraints excluded: chain H residue 2114 LEU Chi-restraints excluded: chain H residue 2205 LEU Chi-restraints excluded: chain H residue 2213 VAL Chi-restraints excluded: chain H residue 2280 LEU Chi-restraints excluded: chain H residue 2284 ASN Chi-restraints excluded: chain H residue 2317 LEU Chi-restraints excluded: chain H residue 2449 ILE Chi-restraints excluded: chain H residue 2451 THR Chi-restraints excluded: chain H residue 2454 ILE Chi-restraints excluded: chain H residue 2505 LYS Chi-restraints excluded: chain H residue 2519 VAL Chi-restraints excluded: chain H residue 2525 LEU Chi-restraints excluded: chain H residue 2532 LEU Chi-restraints excluded: chain H residue 2554 SER Chi-restraints excluded: chain H residue 2693 ILE Chi-restraints excluded: chain H residue 2763 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F1320 ASN ** F1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1320 ASN ** H1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.042896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.030853 restraints weight = 380096.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.031519 restraints weight = 217880.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.031979 restraints weight = 149200.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.032301 restraints weight = 114100.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.032461 restraints weight = 94177.072| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.117 34164 Z= 0.447 Angle : 0.921 15.580 46840 Z= 0.477 Chirality : 0.045 0.281 5844 Planarity : 0.006 0.103 6088 Dihedral : 6.503 65.169 5342 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.58 % Favored : 85.37 % Rotamer: Outliers : 6.37 % Allowed : 17.96 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.29 % 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: -2.50 (0.14), residues: 3506 helix: -0.83 (0.10), residues: 2272 sheet: -3.66 (0.57), residues: 46 loop : -3.14 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H2104 TYR 0.019 0.002 TYR H2700 PHE 0.031 0.003 PHE F2255 TRP 0.045 0.003 TRP H1805 HIS 0.009 0.002 HIS F2533 Details of bonding type rmsd/Z covalent geometry : bond 0.00910 / 0.45 (34164) covalent geometry : angle 0.92139 / 0.48 (46840) hydrogen bonds : bond 0.04463 / 2.45 ( 2080) hydrogen bonds : angle 5.41759 / 2.89 ( 6132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 96 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1530 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.8056 (m-70) REVERT: F 1780 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8640 (t80) REVERT: F 1920 MET cc_start: 0.9283 (mpp) cc_final: 0.8844 (mpp) REVERT: F 1946 LEU cc_start: 0.9463 (tt) cc_final: 0.9083 (tt) REVERT: F 1950 MET cc_start: 0.8911 (mmm) cc_final: 0.8656 (mmm) REVERT: F 2070 MET cc_start: 0.9245 (mmt) cc_final: 0.9002 (mmm) REVERT: F 2477 MET cc_start: 0.9389 (tpp) cc_final: 0.9013 (tpp) REVERT: F 2505 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8711 (mttp) REVERT: F 2753 MET cc_start: 0.8383 (mpp) cc_final: 0.8167 (mpp) REVERT: H 1780 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8636 (t80) REVERT: H 1920 MET cc_start: 0.9266 (mpp) cc_final: 0.8834 (mpp) REVERT: H 1946 LEU cc_start: 0.9469 (tt) cc_final: 0.9093 (tt) REVERT: H 1950 MET cc_start: 0.8923 (mmm) cc_final: 0.8666 (mmm) REVERT: H 2070 MET cc_start: 0.9249 (mmt) cc_final: 0.9014 (mmm) REVERT: H 2205 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9309 (mt) REVERT: H 2477 MET cc_start: 0.9389 (tpp) cc_final: 0.9015 (tpp) REVERT: H 2505 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8707 (mtmm) REVERT: H 2532 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9515 (tt) REVERT: H 2753 MET cc_start: 0.8597 (mpp) cc_final: 0.8267 (mpp) outliers start: 144 outliers final: 83 residues processed: 236 average time/residue: 0.1695 time to fit residues: 72.0089 Evaluate side-chains 182 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 92 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1200 THR Chi-restraints excluded: chain F residue 1259 LEU Chi-restraints excluded: chain F residue 1284 PHE Chi-restraints excluded: chain F residue 1300 THR Chi-restraints excluded: chain F residue 1340 ILE Chi-restraints excluded: chain F residue 1350 THR Chi-restraints excluded: chain F residue 1373 LEU Chi-restraints excluded: chain F residue 1460 ILE Chi-restraints excluded: chain F residue 1471 ASN Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1502 VAL Chi-restraints excluded: chain F residue 1528 GLN Chi-restraints excluded: chain F residue 1530 HIS Chi-restraints excluded: chain F residue 1691 MET Chi-restraints excluded: chain F residue 1694 HIS Chi-restraints excluded: chain F residue 1730 LEU Chi-restraints excluded: chain F residue 1740 LEU Chi-restraints excluded: chain F residue 1771 ILE Chi-restraints excluded: chain F residue 1780 PHE Chi-restraints excluded: chain F residue 1804 THR Chi-restraints excluded: chain F residue 1903 LEU Chi-restraints excluded: chain F residue 1922 THR Chi-restraints excluded: chain F residue 1966 LYS Chi-restraints excluded: chain F residue 2048 LEU Chi-restraints excluded: chain F residue 2052 THR Chi-restraints excluded: chain F residue 2089 ASP Chi-restraints excluded: chain F residue 2105 LEU Chi-restraints excluded: chain F residue 2114 LEU Chi-restraints excluded: chain F residue 2129 ASP Chi-restraints excluded: chain F residue 2213 VAL Chi-restraints excluded: chain F residue 2280 LEU Chi-restraints excluded: chain F residue 2284 ASN Chi-restraints excluded: chain F residue 2290 ILE Chi-restraints excluded: chain F residue 2317 LEU Chi-restraints excluded: chain F residue 2449 ILE Chi-restraints excluded: chain F residue 2451 THR Chi-restraints excluded: chain F residue 2454 ILE Chi-restraints excluded: chain F residue 2463 LEU Chi-restraints excluded: chain F residue 2505 LYS Chi-restraints excluded: chain F residue 2519 VAL Chi-restraints excluded: chain F residue 2554 SER Chi-restraints excluded: chain F residue 2603 ILE Chi-restraints excluded: chain F residue 2763 VAL Chi-restraints excluded: chain H residue 1200 THR Chi-restraints excluded: chain H residue 1259 LEU Chi-restraints excluded: chain H residue 1284 PHE Chi-restraints excluded: chain H residue 1300 THR Chi-restraints excluded: chain H residue 1340 ILE Chi-restraints excluded: chain H residue 1350 THR Chi-restraints excluded: chain H residue 1373 LEU Chi-restraints excluded: chain H residue 1460 ILE Chi-restraints excluded: chain H residue 1471 ASN Chi-restraints excluded: chain H residue 1493 LEU Chi-restraints excluded: chain H residue 1502 VAL Chi-restraints excluded: chain H residue 1528 GLN Chi-restraints excluded: chain H residue 1530 HIS Chi-restraints excluded: chain H residue 1691 MET Chi-restraints excluded: chain H residue 1694 HIS Chi-restraints excluded: chain H residue 1730 LEU Chi-restraints excluded: chain H residue 1740 LEU Chi-restraints excluded: chain H residue 1771 ILE Chi-restraints excluded: chain H residue 1780 PHE Chi-restraints excluded: chain H residue 1804 THR Chi-restraints excluded: chain H residue 1903 LEU Chi-restraints excluded: chain H residue 1922 THR Chi-restraints excluded: chain H residue 1966 LYS Chi-restraints excluded: chain H residue 2048 LEU Chi-restraints excluded: chain H residue 2052 THR Chi-restraints excluded: chain H residue 2089 ASP Chi-restraints excluded: chain H residue 2105 LEU Chi-restraints excluded: chain H residue 2114 LEU Chi-restraints excluded: chain H residue 2129 ASP Chi-restraints excluded: chain H residue 2205 LEU Chi-restraints excluded: chain H residue 2213 VAL Chi-restraints excluded: chain H residue 2280 LEU Chi-restraints excluded: chain H residue 2284 ASN Chi-restraints excluded: chain H residue 2290 ILE Chi-restraints excluded: chain H residue 2317 LEU Chi-restraints excluded: chain H residue 2449 ILE Chi-restraints excluded: chain H residue 2451 THR Chi-restraints excluded: chain H residue 2463 LEU Chi-restraints excluded: chain H residue 2505 LYS Chi-restraints excluded: chain H residue 2519 VAL Chi-restraints excluded: chain H residue 2525 LEU Chi-restraints excluded: chain H residue 2532 LEU Chi-restraints excluded: chain H residue 2554 SER Chi-restraints excluded: chain H residue 2573 LEU Chi-restraints excluded: chain H residue 2603 ILE Chi-restraints excluded: chain H residue 2630 ILE Chi-restraints excluded: chain H residue 2763 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2208 ASN ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.042675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.030746 restraints weight = 378242.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.031398 restraints weight = 219144.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.031876 restraints weight = 149993.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.032167 restraints weight = 114554.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.032413 restraints weight = 95071.749| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.119 34164 Z= 0.444 Angle : 0.923 15.493 46840 Z= 0.477 Chirality : 0.046 0.659 5844 Planarity : 0.006 0.106 6088 Dihedral : 6.480 63.745 5342 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.32 % Favored : 85.62 % Rotamer: Outliers : 6.64 % Allowed : 18.94 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.29 % 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: -2.60 (0.13), residues: 3506 helix: -0.89 (0.10), residues: 2280 sheet: -3.87 (0.54), residues: 46 loop : -3.20 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F2389 TYR 0.019 0.002 TYR F1084 PHE 0.027 0.003 PHE F2255 TRP 0.029 0.003 TRP H1805 HIS 0.008 0.002 HIS H2533 Details of bonding type rmsd/Z covalent geometry : bond 0.00905 / 0.44 (34164) covalent geometry : angle 0.92311 / 0.48 (46840) hydrogen bonds : bond 0.04420 / 2.43 ( 2080) hydrogen bonds : angle 5.45925 / 2.92 ( 6132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 93 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1530 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.8049 (m-70) REVERT: F 1780 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8640 (t80) REVERT: F 1920 MET cc_start: 0.9295 (mpp) cc_final: 0.8854 (mpp) REVERT: F 1946 LEU cc_start: 0.9477 (tt) cc_final: 0.9028 (tt) REVERT: F 1950 MET cc_start: 0.8966 (mmm) cc_final: 0.8696 (mmm) REVERT: F 2070 MET cc_start: 0.9291 (mmt) cc_final: 0.8946 (mmm) REVERT: F 2477 MET cc_start: 0.9392 (tpp) cc_final: 0.9012 (tpp) REVERT: F 2505 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8746 (mttp) REVERT: F 2753 MET cc_start: 0.8414 (mpp) cc_final: 0.8209 (mpp) REVERT: H 1530 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.8357 (m-70) REVERT: H 1780 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8637 (t80) REVERT: H 1920 MET cc_start: 0.9303 (mpp) cc_final: 0.8856 (mpp) REVERT: H 1946 LEU cc_start: 0.9481 (tt) cc_final: 0.9034 (tt) REVERT: H 1950 MET cc_start: 0.8976 (mmm) cc_final: 0.8702 (mmm) REVERT: H 2070 MET cc_start: 0.9292 (mmt) cc_final: 0.9057 (mmm) REVERT: H 2205 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9305 (mt) REVERT: H 2477 MET cc_start: 0.9388 (tpp) cc_final: 0.9010 (tpp) REVERT: H 2505 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8760 (mttm) REVERT: H 2753 MET cc_start: 0.8662 (mpp) cc_final: 0.8278 (mpp) outliers start: 150 outliers final: 98 residues processed: 239 average time/residue: 0.1697 time to fit residues: 71.9840 Evaluate side-chains 198 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 93 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1192 ILE Chi-restraints excluded: chain F residue 1200 THR Chi-restraints excluded: chain F residue 1259 LEU Chi-restraints excluded: chain F residue 1284 PHE Chi-restraints excluded: chain F residue 1300 THR Chi-restraints excluded: chain F residue 1350 THR Chi-restraints excluded: chain F residue 1373 LEU Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1460 ILE Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1502 VAL Chi-restraints excluded: chain F residue 1522 VAL Chi-restraints excluded: chain F residue 1528 GLN Chi-restraints excluded: chain F residue 1530 HIS Chi-restraints excluded: chain F residue 1649 TYR Chi-restraints excluded: chain F residue 1691 MET Chi-restraints excluded: chain F residue 1694 HIS Chi-restraints excluded: chain F residue 1730 LEU Chi-restraints excluded: chain F residue 1771 ILE Chi-restraints excluded: chain F residue 1780 PHE Chi-restraints excluded: chain F residue 1804 THR Chi-restraints excluded: chain F residue 1856 VAL Chi-restraints excluded: chain F residue 1865 ASP Chi-restraints excluded: chain F residue 1892 VAL Chi-restraints excluded: chain F residue 1903 LEU Chi-restraints excluded: chain F residue 1922 THR Chi-restraints excluded: chain F residue 1966 LYS Chi-restraints excluded: chain F residue 1967 THR Chi-restraints excluded: chain F residue 1999 ILE Chi-restraints excluded: chain F residue 2048 LEU Chi-restraints excluded: chain F residue 2089 ASP Chi-restraints excluded: chain F residue 2105 LEU Chi-restraints excluded: chain F residue 2108 TRP Chi-restraints excluded: chain F residue 2114 LEU Chi-restraints excluded: chain F residue 2129 ASP Chi-restraints excluded: chain F residue 2213 VAL Chi-restraints excluded: chain F residue 2268 TYR Chi-restraints excluded: chain F residue 2280 LEU Chi-restraints excluded: chain F residue 2284 ASN Chi-restraints excluded: chain F residue 2301 LEU Chi-restraints excluded: chain F residue 2317 LEU Chi-restraints excluded: chain F residue 2449 ILE Chi-restraints excluded: chain F residue 2451 THR Chi-restraints excluded: chain F residue 2454 ILE Chi-restraints excluded: chain F residue 2463 LEU Chi-restraints excluded: chain F residue 2505 LYS Chi-restraints excluded: chain F residue 2554 SER Chi-restraints excluded: chain F residue 2565 ILE Chi-restraints excluded: chain F residue 2603 ILE Chi-restraints excluded: chain F residue 2693 ILE Chi-restraints excluded: chain F residue 2763 VAL Chi-restraints excluded: chain H residue 1192 ILE Chi-restraints excluded: chain H residue 1200 THR Chi-restraints excluded: chain H residue 1259 LEU Chi-restraints excluded: chain H residue 1284 PHE Chi-restraints excluded: chain H residue 1300 THR Chi-restraints excluded: chain H residue 1340 ILE Chi-restraints excluded: chain H residue 1350 THR Chi-restraints excluded: chain H residue 1373 LEU Chi-restraints excluded: chain H residue 1397 LEU Chi-restraints excluded: chain H residue 1460 ILE Chi-restraints excluded: chain H residue 1493 LEU Chi-restraints excluded: chain H residue 1502 VAL Chi-restraints excluded: chain H residue 1522 VAL Chi-restraints excluded: chain H residue 1530 HIS Chi-restraints excluded: chain H residue 1649 TYR Chi-restraints excluded: chain H residue 1691 MET Chi-restraints excluded: chain H residue 1694 HIS Chi-restraints excluded: chain H residue 1730 LEU Chi-restraints excluded: chain H residue 1771 ILE Chi-restraints excluded: chain H residue 1780 PHE Chi-restraints excluded: chain H residue 1804 THR Chi-restraints excluded: chain H residue 1856 VAL Chi-restraints excluded: chain H residue 1865 ASP Chi-restraints excluded: chain H residue 1892 VAL Chi-restraints excluded: chain H residue 1903 LEU Chi-restraints excluded: chain H residue 1922 THR Chi-restraints excluded: chain H residue 1966 LYS Chi-restraints excluded: chain H residue 1967 THR Chi-restraints excluded: chain H residue 1999 ILE Chi-restraints excluded: chain H residue 2048 LEU Chi-restraints excluded: chain H residue 2089 ASP Chi-restraints excluded: chain H residue 2105 LEU Chi-restraints excluded: chain H residue 2108 TRP Chi-restraints excluded: chain H residue 2114 LEU Chi-restraints excluded: chain H residue 2129 ASP Chi-restraints excluded: chain H residue 2205 LEU Chi-restraints excluded: chain H residue 2213 VAL Chi-restraints excluded: chain H residue 2268 TYR Chi-restraints excluded: chain H residue 2280 LEU Chi-restraints excluded: chain H residue 2284 ASN Chi-restraints excluded: chain H residue 2317 LEU Chi-restraints excluded: chain H residue 2390 LEU Chi-restraints excluded: chain H residue 2411 PRO Chi-restraints excluded: chain H residue 2449 ILE Chi-restraints excluded: chain H residue 2451 THR Chi-restraints excluded: chain H residue 2454 ILE Chi-restraints excluded: chain H residue 2463 LEU Chi-restraints excluded: chain H residue 2505 LYS Chi-restraints excluded: chain H residue 2525 LEU Chi-restraints excluded: chain H residue 2554 SER Chi-restraints excluded: chain H residue 2565 ILE Chi-restraints excluded: chain H residue 2603 ILE Chi-restraints excluded: chain H residue 2693 ILE Chi-restraints excluded: chain H residue 2763 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.042561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.030576 restraints weight = 382689.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.031250 restraints weight = 219691.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.031724 restraints weight = 150189.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.032039 restraints weight = 114401.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.032224 restraints weight = 94529.968| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.124 34164 Z= 0.488 Angle : 0.961 16.665 46840 Z= 0.498 Chirality : 0.046 0.358 5844 Planarity : 0.006 0.106 6088 Dihedral : 6.585 63.967 5342 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.74 % Favored : 84.20 % Rotamer: Outliers : 6.73 % Allowed : 19.91 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.29 % 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: -2.77 (0.13), residues: 3506 helix: -1.04 (0.10), residues: 2278 sheet: -3.96 (0.54), residues: 46 loop : -3.22 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H2613 TYR 0.019 0.003 TYR F1244 PHE 0.027 0.003 PHE F1576 TRP 0.034 0.003 TRP H1805 HIS 0.010 0.002 HIS H2533 Details of bonding type rmsd/Z covalent geometry : bond 0.00989 / 0.49 (34164) covalent geometry : angle 0.96144 / 0.50 (46840) hydrogen bonds : bond 0.04620 / 2.54 ( 2080) hydrogen bonds : angle 5.59607 / 3.00 ( 6132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 95 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1780 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8667 (t80) REVERT: F 1920 MET cc_start: 0.9310 (mpp) cc_final: 0.8851 (mpp) REVERT: F 1946 LEU cc_start: 0.9515 (tt) cc_final: 0.9035 (tt) REVERT: F 1950 MET cc_start: 0.8986 (mmm) cc_final: 0.8708 (mmm) REVERT: F 2070 MET cc_start: 0.9338 (mmt) cc_final: 0.9075 (mmm) REVERT: F 2155 LYS cc_start: 0.9779 (OUTLIER) cc_final: 0.9544 (ptmm) REVERT: F 2471 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9039 (mp) REVERT: F 2477 MET cc_start: 0.9386 (tpp) cc_final: 0.9011 (tpp) REVERT: F 2505 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8770 (mttp) REVERT: F 2753 MET cc_start: 0.8460 (mpp) cc_final: 0.8252 (mpp) REVERT: H 1530 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8270 (m-70) REVERT: H 1780 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8628 (t80) REVERT: H 1920 MET cc_start: 0.9322 (mpp) cc_final: 0.8852 (mpp) REVERT: H 1946 LEU cc_start: 0.9519 (tt) cc_final: 0.9039 (tt) REVERT: H 1950 MET cc_start: 0.8995 (mmm) cc_final: 0.8716 (mmm) REVERT: H 2070 MET cc_start: 0.9340 (mmt) cc_final: 0.9080 (mmm) REVERT: H 2155 LYS cc_start: 0.9776 (OUTLIER) cc_final: 0.9543 (ptmm) REVERT: H 2205 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9306 (mt) REVERT: H 2471 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9041 (mp) REVERT: H 2477 MET cc_start: 0.9389 (tpp) cc_final: 0.9013 (tpp) REVERT: H 2505 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8802 (mttm) REVERT: H 2753 MET cc_start: 0.8721 (mpp) cc_final: 0.8259 (mpp) outliers start: 152 outliers final: 115 residues processed: 243 average time/residue: 0.1671 time to fit residues: 72.4612 Evaluate side-chains 218 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 93 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1192 ILE Chi-restraints excluded: chain F residue 1200 THR Chi-restraints excluded: chain F residue 1259 LEU Chi-restraints excluded: chain F residue 1284 PHE Chi-restraints excluded: chain F residue 1300 THR Chi-restraints excluded: chain F residue 1340 ILE Chi-restraints excluded: chain F residue 1350 THR Chi-restraints excluded: chain F residue 1373 LEU Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1440 ASP Chi-restraints excluded: chain F residue 1460 ILE Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1502 VAL Chi-restraints excluded: chain F residue 1522 VAL Chi-restraints excluded: chain F residue 1530 HIS Chi-restraints excluded: chain F residue 1649 TYR Chi-restraints excluded: chain F residue 1691 MET Chi-restraints excluded: chain F residue 1694 HIS Chi-restraints excluded: chain F residue 1730 LEU Chi-restraints excluded: chain F residue 1740 LEU Chi-restraints excluded: chain F residue 1771 ILE Chi-restraints excluded: chain F residue 1780 PHE Chi-restraints excluded: chain F residue 1804 THR Chi-restraints excluded: chain F residue 1856 VAL Chi-restraints excluded: chain F residue 1865 ASP Chi-restraints excluded: chain F residue 1892 VAL Chi-restraints excluded: chain F residue 1903 LEU Chi-restraints excluded: chain F residue 1922 THR Chi-restraints excluded: chain F residue 1966 LYS Chi-restraints excluded: chain F residue 1967 THR Chi-restraints excluded: chain F residue 1999 ILE Chi-restraints excluded: chain F residue 2006 VAL Chi-restraints excluded: chain F residue 2048 LEU Chi-restraints excluded: chain F residue 2089 ASP Chi-restraints excluded: chain F residue 2105 LEU Chi-restraints excluded: chain F residue 2108 TRP Chi-restraints excluded: chain F residue 2114 LEU Chi-restraints excluded: chain F residue 2129 ASP Chi-restraints excluded: chain F residue 2155 LYS Chi-restraints excluded: chain F residue 2213 VAL Chi-restraints excluded: chain F residue 2242 TYR Chi-restraints excluded: chain F residue 2268 TYR Chi-restraints excluded: chain F residue 2280 LEU Chi-restraints excluded: chain F residue 2284 ASN Chi-restraints excluded: chain F residue 2301 LEU Chi-restraints excluded: chain F residue 2317 LEU Chi-restraints excluded: chain F residue 2345 LYS Chi-restraints excluded: chain F residue 2449 ILE Chi-restraints excluded: chain F residue 2451 THR Chi-restraints excluded: chain F residue 2454 ILE Chi-restraints excluded: chain F residue 2463 LEU Chi-restraints excluded: chain F residue 2471 LEU Chi-restraints excluded: chain F residue 2505 LYS Chi-restraints excluded: chain F residue 2519 VAL Chi-restraints excluded: chain F residue 2536 ASP Chi-restraints excluded: chain F residue 2554 SER Chi-restraints excluded: chain F residue 2565 ILE Chi-restraints excluded: chain F residue 2603 ILE Chi-restraints excluded: chain F residue 2693 ILE Chi-restraints excluded: chain F residue 2763 VAL Chi-restraints excluded: chain H residue 1192 ILE Chi-restraints excluded: chain H residue 1200 THR Chi-restraints excluded: chain H residue 1259 LEU Chi-restraints excluded: chain H residue 1284 PHE Chi-restraints excluded: chain H residue 1300 THR Chi-restraints excluded: chain H residue 1350 THR Chi-restraints excluded: chain H residue 1373 LEU Chi-restraints excluded: chain H residue 1397 LEU Chi-restraints excluded: chain H residue 1460 ILE Chi-restraints excluded: chain H residue 1493 LEU Chi-restraints excluded: chain H residue 1502 VAL Chi-restraints excluded: chain H residue 1522 VAL Chi-restraints excluded: chain H residue 1530 HIS Chi-restraints excluded: chain H residue 1649 TYR Chi-restraints excluded: chain H residue 1691 MET Chi-restraints excluded: chain H residue 1694 HIS Chi-restraints excluded: chain H residue 1730 LEU Chi-restraints excluded: chain H residue 1740 LEU Chi-restraints excluded: chain H residue 1771 ILE Chi-restraints excluded: chain H residue 1780 PHE Chi-restraints excluded: chain H residue 1804 THR Chi-restraints excluded: chain H residue 1856 VAL Chi-restraints excluded: chain H residue 1865 ASP Chi-restraints excluded: chain H residue 1892 VAL Chi-restraints excluded: chain H residue 1903 LEU Chi-restraints excluded: chain H residue 1922 THR Chi-restraints excluded: chain H residue 1927 ILE Chi-restraints excluded: chain H residue 1966 LYS Chi-restraints excluded: chain H residue 1967 THR Chi-restraints excluded: chain H residue 1999 ILE Chi-restraints excluded: chain H residue 2006 VAL Chi-restraints excluded: chain H residue 2048 LEU Chi-restraints excluded: chain H residue 2089 ASP Chi-restraints excluded: chain H residue 2105 LEU Chi-restraints excluded: chain H residue 2108 TRP Chi-restraints excluded: chain H residue 2114 LEU Chi-restraints excluded: chain H residue 2129 ASP Chi-restraints excluded: chain H residue 2155 LYS Chi-restraints excluded: chain H residue 2205 LEU Chi-restraints excluded: chain H residue 2213 VAL Chi-restraints excluded: chain H residue 2242 TYR Chi-restraints excluded: chain H residue 2268 TYR Chi-restraints excluded: chain H residue 2280 LEU Chi-restraints excluded: chain H residue 2284 ASN Chi-restraints excluded: chain H residue 2301 LEU Chi-restraints excluded: chain H residue 2317 LEU Chi-restraints excluded: chain H residue 2345 LYS Chi-restraints excluded: chain H residue 2390 LEU Chi-restraints excluded: chain H residue 2411 PRO Chi-restraints excluded: chain H residue 2449 ILE Chi-restraints excluded: chain H residue 2451 THR Chi-restraints excluded: chain H residue 2454 ILE Chi-restraints excluded: chain H residue 2463 LEU Chi-restraints excluded: chain H residue 2471 LEU Chi-restraints excluded: chain H residue 2487 VAL Chi-restraints excluded: chain H residue 2501 ILE Chi-restraints excluded: chain H residue 2505 LYS Chi-restraints excluded: chain H residue 2519 VAL Chi-restraints excluded: chain H residue 2525 LEU Chi-restraints excluded: chain H residue 2554 SER Chi-restraints excluded: chain H residue 2565 ILE Chi-restraints excluded: chain H residue 2603 ILE Chi-restraints excluded: chain H residue 2630 ILE Chi-restraints excluded: chain H residue 2693 ILE Chi-restraints excluded: chain H residue 2763 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.042454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.030463 restraints weight = 380146.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.031139 restraints weight = 219761.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.031606 restraints weight = 150186.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.031887 restraints weight = 114480.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032129 restraints weight = 95264.693| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.124 34164 Z= 0.489 Angle : 0.969 16.506 46840 Z= 0.501 Chirality : 0.046 0.369 5844 Planarity : 0.006 0.106 6088 Dihedral : 6.612 63.458 5342 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.69 % Favored : 84.26 % Rotamer: Outliers : 6.95 % Allowed : 20.44 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.29 % 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: -2.82 (0.13), residues: 3506 helix: -1.08 (0.10), residues: 2274 sheet: -4.56 (0.55), residues: 32 loop : -3.25 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F2613 TYR 0.021 0.003 TYR F1244 PHE 0.026 0.003 PHE H1576 TRP 0.031 0.003 TRP H1805 HIS 0.011 0.002 HIS H1525 Details of bonding type rmsd/Z covalent geometry : bond 0.00991 / 0.49 (34164) covalent geometry : angle 0.96873 / 0.50 (46840) hydrogen bonds : bond 0.04654 / 2.56 ( 2080) hydrogen bonds : angle 5.63409 / 3.02 ( 6132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 94 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1530 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.8231 (m-70) REVERT: F 1711 MET cc_start: 0.9095 (tmm) cc_final: 0.8874 (ppp) REVERT: F 1780 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8673 (t80) REVERT: F 1920 MET cc_start: 0.9307 (mpp) cc_final: 0.8844 (mpp) REVERT: F 1946 LEU cc_start: 0.9550 (tt) cc_final: 0.9134 (tt) REVERT: F 1950 MET cc_start: 0.8986 (mmm) cc_final: 0.8730 (mmm) REVERT: F 2070 MET cc_start: 0.9341 (mmt) cc_final: 0.9086 (mmm) REVERT: F 2155 LYS cc_start: 0.9777 (OUTLIER) cc_final: 0.9536 (ptmm) REVERT: F 2372 MET cc_start: 0.9153 (mmm) cc_final: 0.8727 (mmm) REVERT: F 2471 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9053 (mp) REVERT: F 2477 MET cc_start: 0.9391 (tpp) cc_final: 0.9024 (tpp) REVERT: F 2505 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8824 (mtmm) REVERT: F 2547 MET cc_start: 0.9313 (ppp) cc_final: 0.9106 (ppp) REVERT: F 2704 MET cc_start: 0.8330 (tpp) cc_final: 0.8066 (tpt) REVERT: F 2753 MET cc_start: 0.8453 (mpp) cc_final: 0.8240 (mpp) REVERT: H 1711 MET cc_start: 0.9097 (tmm) cc_final: 0.8874 (ppp) REVERT: H 1780 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8645 (t80) REVERT: H 1920 MET cc_start: 0.9310 (mpp) cc_final: 0.8837 (mpp) REVERT: H 1946 LEU cc_start: 0.9553 (tt) cc_final: 0.9137 (tt) REVERT: H 1950 MET cc_start: 0.8993 (mmm) cc_final: 0.8737 (mmm) REVERT: H 2070 MET cc_start: 0.9347 (mmt) cc_final: 0.9092 (mmm) REVERT: H 2155 LYS cc_start: 0.9775 (OUTLIER) cc_final: 0.9537 (ptmm) REVERT: H 2205 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9301 (mt) REVERT: H 2298 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7197 (tp-100) REVERT: H 2372 MET cc_start: 0.9139 (mmm) cc_final: 0.8729 (mmm) REVERT: H 2471 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9051 (mp) REVERT: H 2477 MET cc_start: 0.9391 (tpp) cc_final: 0.9023 (tpp) REVERT: H 2505 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8833 (mtmm) REVERT: H 2753 MET cc_start: 0.8695 (mpp) cc_final: 0.8418 (mpp) outliers start: 157 outliers final: 116 residues processed: 247 average time/residue: 0.1595 time to fit residues: 70.2886 Evaluate side-chains 218 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 91 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1192 ILE Chi-restraints excluded: chain F residue 1200 THR Chi-restraints excluded: chain F residue 1259 LEU Chi-restraints excluded: chain F residue 1284 PHE Chi-restraints excluded: chain F residue 1300 THR Chi-restraints excluded: chain F residue 1350 THR Chi-restraints excluded: chain F residue 1373 LEU Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1440 ASP Chi-restraints excluded: chain F residue 1460 ILE Chi-restraints excluded: chain F residue 1502 VAL Chi-restraints excluded: chain F residue 1522 VAL Chi-restraints excluded: chain F residue 1530 HIS Chi-restraints excluded: chain F residue 1649 TYR Chi-restraints excluded: chain F residue 1691 MET Chi-restraints excluded: chain F residue 1694 HIS Chi-restraints excluded: chain F residue 1730 LEU Chi-restraints excluded: chain F residue 1740 LEU Chi-restraints excluded: chain F residue 1771 ILE Chi-restraints excluded: chain F residue 1780 PHE Chi-restraints excluded: chain F residue 1804 THR Chi-restraints excluded: chain F residue 1856 VAL Chi-restraints excluded: chain F residue 1865 ASP Chi-restraints excluded: chain F residue 1892 VAL Chi-restraints excluded: chain F residue 1903 LEU Chi-restraints excluded: chain F residue 1922 THR Chi-restraints excluded: chain F residue 1966 LYS Chi-restraints excluded: chain F residue 1967 THR Chi-restraints excluded: chain F residue 1999 ILE Chi-restraints excluded: chain F residue 2006 VAL Chi-restraints excluded: chain F residue 2048 LEU Chi-restraints excluded: chain F residue 2089 ASP Chi-restraints excluded: chain F residue 2105 LEU Chi-restraints excluded: chain F residue 2108 TRP Chi-restraints excluded: chain F residue 2114 LEU Chi-restraints excluded: chain F residue 2129 ASP Chi-restraints excluded: chain F residue 2155 LYS Chi-restraints excluded: chain F residue 2213 VAL Chi-restraints excluded: chain F residue 2242 TYR Chi-restraints excluded: chain F residue 2268 TYR Chi-restraints excluded: chain F residue 2280 LEU Chi-restraints excluded: chain F residue 2284 ASN Chi-restraints excluded: chain F residue 2290 ILE Chi-restraints excluded: chain F residue 2301 LEU Chi-restraints excluded: chain F residue 2317 LEU Chi-restraints excluded: chain F residue 2345 LYS Chi-restraints excluded: chain F residue 2449 ILE Chi-restraints excluded: chain F residue 2451 THR Chi-restraints excluded: chain F residue 2454 ILE Chi-restraints excluded: chain F residue 2463 LEU Chi-restraints excluded: chain F residue 2471 LEU Chi-restraints excluded: chain F residue 2487 VAL Chi-restraints excluded: chain F residue 2505 LYS Chi-restraints excluded: chain F residue 2519 VAL Chi-restraints excluded: chain F residue 2536 ASP Chi-restraints excluded: chain F residue 2554 SER Chi-restraints excluded: chain F residue 2565 ILE Chi-restraints excluded: chain F residue 2603 ILE Chi-restraints excluded: chain F residue 2693 ILE Chi-restraints excluded: chain F residue 2763 VAL Chi-restraints excluded: chain H residue 1192 ILE Chi-restraints excluded: chain H residue 1200 THR Chi-restraints excluded: chain H residue 1259 LEU Chi-restraints excluded: chain H residue 1284 PHE Chi-restraints excluded: chain H residue 1300 THR Chi-restraints excluded: chain H residue 1350 THR Chi-restraints excluded: chain H residue 1397 LEU Chi-restraints excluded: chain H residue 1408 THR Chi-restraints excluded: chain H residue 1440 ASP Chi-restraints excluded: chain H residue 1460 ILE Chi-restraints excluded: chain H residue 1493 LEU Chi-restraints excluded: chain H residue 1502 VAL Chi-restraints excluded: chain H residue 1522 VAL Chi-restraints excluded: chain H residue 1530 HIS Chi-restraints excluded: chain H residue 1649 TYR Chi-restraints excluded: chain H residue 1691 MET Chi-restraints excluded: chain H residue 1694 HIS Chi-restraints excluded: chain H residue 1730 LEU Chi-restraints excluded: chain H residue 1740 LEU Chi-restraints excluded: chain H residue 1771 ILE Chi-restraints excluded: chain H residue 1780 PHE Chi-restraints excluded: chain H residue 1804 THR Chi-restraints excluded: chain H residue 1856 VAL Chi-restraints excluded: chain H residue 1865 ASP Chi-restraints excluded: chain H residue 1892 VAL Chi-restraints excluded: chain H residue 1903 LEU Chi-restraints excluded: chain H residue 1922 THR Chi-restraints excluded: chain H residue 1927 ILE Chi-restraints excluded: chain H residue 1966 LYS Chi-restraints excluded: chain H residue 1967 THR Chi-restraints excluded: chain H residue 1999 ILE Chi-restraints excluded: chain H residue 2006 VAL Chi-restraints excluded: chain H residue 2048 LEU Chi-restraints excluded: chain H residue 2089 ASP Chi-restraints excluded: chain H residue 2105 LEU Chi-restraints excluded: chain H residue 2108 TRP Chi-restraints excluded: chain H residue 2114 LEU Chi-restraints excluded: chain H residue 2129 ASP Chi-restraints excluded: chain H residue 2155 LYS Chi-restraints excluded: chain H residue 2205 LEU Chi-restraints excluded: chain H residue 2213 VAL Chi-restraints excluded: chain H residue 2242 TYR Chi-restraints excluded: chain H residue 2268 TYR Chi-restraints excluded: chain H residue 2280 LEU Chi-restraints excluded: chain H residue 2284 ASN Chi-restraints excluded: chain H residue 2298 GLN Chi-restraints excluded: chain H residue 2301 LEU Chi-restraints excluded: chain H residue 2317 LEU Chi-restraints excluded: chain H residue 2345 LYS Chi-restraints excluded: chain H residue 2390 LEU Chi-restraints excluded: chain H residue 2411 PRO Chi-restraints excluded: chain H residue 2449 ILE Chi-restraints excluded: chain H residue 2451 THR Chi-restraints excluded: chain H residue 2454 ILE Chi-restraints excluded: chain H residue 2463 LEU Chi-restraints excluded: chain H residue 2471 LEU Chi-restraints excluded: chain H residue 2487 VAL Chi-restraints excluded: chain H residue 2501 ILE Chi-restraints excluded: chain H residue 2505 LYS Chi-restraints excluded: chain H residue 2519 VAL Chi-restraints excluded: chain H residue 2525 LEU Chi-restraints excluded: chain H residue 2554 SER Chi-restraints excluded: chain H residue 2565 ILE Chi-restraints excluded: chain H residue 2603 ILE Chi-restraints excluded: chain H residue 2630 ILE Chi-restraints excluded: chain H residue 2693 ILE Chi-restraints excluded: chain H residue 2763 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.042376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.030386 restraints weight = 379952.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.031053 restraints weight = 219685.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.031525 restraints weight = 150305.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.031847 restraints weight = 114262.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.032030 restraints weight = 94358.080| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.127 34164 Z= 0.489 Angle : 0.973 16.397 46840 Z= 0.502 Chirality : 0.047 0.402 5844 Planarity : 0.006 0.106 6088 Dihedral : 6.598 63.405 5340 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 16.09 % Favored : 83.77 % Rotamer: Outliers : 6.28 % Allowed : 21.37 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.32 % 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: -2.83 (0.13), residues: 3506 helix: -1.10 (0.10), residues: 2280 sheet: -3.97 (0.56), residues: 46 loop : -3.23 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F2613 TYR 0.021 0.003 TYR F1244 PHE 0.025 0.003 PHE F1576 TRP 0.036 0.003 TRP F1805 HIS 0.013 0.002 HIS F1525 Details of bonding type rmsd/Z covalent geometry : bond 0.00992 / 0.49 (34164) covalent geometry : angle 0.97306 / 0.50 (46840) hydrogen bonds : bond 0.04701 / 2.58 ( 2080) hydrogen bonds : angle 5.66239 / 3.03 ( 6132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 94 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1704 MET cc_start: 0.9144 (mmm) cc_final: 0.8921 (mmm) REVERT: F 1780 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8675 (t80) REVERT: F 1920 MET cc_start: 0.9312 (mpp) cc_final: 0.8847 (mpp) REVERT: F 1946 LEU cc_start: 0.9541 (tt) cc_final: 0.9095 (tt) REVERT: F 1950 MET cc_start: 0.9012 (mmm) cc_final: 0.8739 (mmm) REVERT: F 2070 MET cc_start: 0.9353 (mmt) cc_final: 0.9100 (mmm) REVERT: F 2298 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8422 (tp40) REVERT: F 2471 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9055 (mp) REVERT: F 2477 MET cc_start: 0.9380 (tpp) cc_final: 0.8989 (tpp) REVERT: F 2505 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8782 (mtmm) REVERT: F 2704 MET cc_start: 0.8309 (tpp) cc_final: 0.7982 (tpt) REVERT: F 2753 MET cc_start: 0.8412 (mpp) cc_final: 0.8207 (mpp) REVERT: H 1530 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8236 (m-70) REVERT: H 1704 MET cc_start: 0.9164 (mmm) cc_final: 0.8939 (mmm) REVERT: H 1780 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8649 (t80) REVERT: H 1920 MET cc_start: 0.9296 (mpp) cc_final: 0.8830 (mpp) REVERT: H 1946 LEU cc_start: 0.9546 (tt) cc_final: 0.9104 (tt) REVERT: H 1950 MET cc_start: 0.9020 (mmm) cc_final: 0.8752 (mmm) REVERT: H 2070 MET cc_start: 0.9352 (mmt) cc_final: 0.9101 (mmm) REVERT: H 2205 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9321 (mt) REVERT: H 2471 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9056 (mp) REVERT: H 2477 MET cc_start: 0.9365 (tpp) cc_final: 0.8970 (tpp) REVERT: H 2505 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8801 (mtmm) REVERT: H 2704 MET cc_start: 0.8717 (ttm) cc_final: 0.8196 (tpt) REVERT: H 2753 MET cc_start: 0.8753 (mpp) cc_final: 0.8406 (mpp) outliers start: 142 outliers final: 115 residues processed: 234 average time/residue: 0.1650 time to fit residues: 69.0172 Evaluate side-chains 217 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 93 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1192 ILE Chi-restraints excluded: chain F residue 1259 LEU Chi-restraints excluded: chain F residue 1284 PHE Chi-restraints excluded: chain F residue 1300 THR Chi-restraints excluded: chain F residue 1350 THR Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1440 ASP Chi-restraints excluded: chain F residue 1460 ILE Chi-restraints excluded: chain F residue 1464 LEU Chi-restraints excluded: chain F residue 1502 VAL Chi-restraints excluded: chain F residue 1522 VAL Chi-restraints excluded: chain F residue 1649 TYR Chi-restraints excluded: chain F residue 1691 MET Chi-restraints excluded: chain F residue 1694 HIS Chi-restraints excluded: chain F residue 1730 LEU Chi-restraints excluded: chain F residue 1740 LEU Chi-restraints excluded: chain F residue 1771 ILE Chi-restraints excluded: chain F residue 1780 PHE Chi-restraints excluded: chain F residue 1804 THR Chi-restraints excluded: chain F residue 1856 VAL Chi-restraints excluded: chain F residue 1865 ASP Chi-restraints excluded: chain F residue 1892 VAL Chi-restraints excluded: chain F residue 1903 LEU Chi-restraints excluded: chain F residue 1922 THR Chi-restraints excluded: chain F residue 1949 ILE Chi-restraints excluded: chain F residue 1966 LYS Chi-restraints excluded: chain F residue 1967 THR Chi-restraints excluded: chain F residue 1999 ILE Chi-restraints excluded: chain F residue 2006 VAL Chi-restraints excluded: chain F residue 2048 LEU Chi-restraints excluded: chain F residue 2089 ASP Chi-restraints excluded: chain F residue 2105 LEU Chi-restraints excluded: chain F residue 2108 TRP Chi-restraints excluded: chain F residue 2114 LEU Chi-restraints excluded: chain F residue 2129 ASP Chi-restraints excluded: chain F residue 2213 VAL Chi-restraints excluded: chain F residue 2242 TYR Chi-restraints excluded: chain F residue 2268 TYR Chi-restraints excluded: chain F residue 2280 LEU Chi-restraints excluded: chain F residue 2284 ASN Chi-restraints excluded: chain F residue 2298 GLN Chi-restraints excluded: chain F residue 2301 LEU Chi-restraints excluded: chain F residue 2317 LEU Chi-restraints excluded: chain F residue 2345 LYS Chi-restraints excluded: chain F residue 2449 ILE Chi-restraints excluded: chain F residue 2451 THR Chi-restraints excluded: chain F residue 2454 ILE Chi-restraints excluded: chain F residue 2463 LEU Chi-restraints excluded: chain F residue 2471 LEU Chi-restraints excluded: chain F residue 2487 VAL Chi-restraints excluded: chain F residue 2505 LYS Chi-restraints excluded: chain F residue 2519 VAL Chi-restraints excluded: chain F residue 2536 ASP Chi-restraints excluded: chain F residue 2554 SER Chi-restraints excluded: chain F residue 2565 ILE Chi-restraints excluded: chain F residue 2603 ILE Chi-restraints excluded: chain F residue 2630 ILE Chi-restraints excluded: chain F residue 2693 ILE Chi-restraints excluded: chain F residue 2763 VAL Chi-restraints excluded: chain H residue 1192 ILE Chi-restraints excluded: chain H residue 1259 LEU Chi-restraints excluded: chain H residue 1284 PHE Chi-restraints excluded: chain H residue 1300 THR Chi-restraints excluded: chain H residue 1350 THR Chi-restraints excluded: chain H residue 1397 LEU Chi-restraints excluded: chain H residue 1408 THR Chi-restraints excluded: chain H residue 1440 ASP Chi-restraints excluded: chain H residue 1460 ILE Chi-restraints excluded: chain H residue 1464 LEU Chi-restraints excluded: chain H residue 1502 VAL Chi-restraints excluded: chain H residue 1522 VAL Chi-restraints excluded: chain H residue 1530 HIS Chi-restraints excluded: chain H residue 1649 TYR Chi-restraints excluded: chain H residue 1691 MET Chi-restraints excluded: chain H residue 1694 HIS Chi-restraints excluded: chain H residue 1730 LEU Chi-restraints excluded: chain H residue 1740 LEU Chi-restraints excluded: chain H residue 1771 ILE Chi-restraints excluded: chain H residue 1780 PHE Chi-restraints excluded: chain H residue 1804 THR Chi-restraints excluded: chain H residue 1856 VAL Chi-restraints excluded: chain H residue 1865 ASP Chi-restraints excluded: chain H residue 1892 VAL Chi-restraints excluded: chain H residue 1903 LEU Chi-restraints excluded: chain H residue 1922 THR Chi-restraints excluded: chain H residue 1949 ILE Chi-restraints excluded: chain H residue 1966 LYS Chi-restraints excluded: chain H residue 1967 THR Chi-restraints excluded: chain H residue 1999 ILE Chi-restraints excluded: chain H residue 2006 VAL Chi-restraints excluded: chain H residue 2048 LEU Chi-restraints excluded: chain H residue 2089 ASP Chi-restraints excluded: chain H residue 2105 LEU Chi-restraints excluded: chain H residue 2108 TRP Chi-restraints excluded: chain H residue 2114 LEU Chi-restraints excluded: chain H residue 2129 ASP Chi-restraints excluded: chain H residue 2205 LEU Chi-restraints excluded: chain H residue 2213 VAL Chi-restraints excluded: chain H residue 2242 TYR Chi-restraints excluded: chain H residue 2268 TYR Chi-restraints excluded: chain H residue 2280 LEU Chi-restraints excluded: chain H residue 2284 ASN Chi-restraints excluded: chain H residue 2301 LEU Chi-restraints excluded: chain H residue 2317 LEU Chi-restraints excluded: chain H residue 2345 LYS Chi-restraints excluded: chain H residue 2390 LEU Chi-restraints excluded: chain H residue 2435 GLU Chi-restraints excluded: chain H residue 2449 ILE Chi-restraints excluded: chain H residue 2451 THR Chi-restraints excluded: chain H residue 2454 ILE Chi-restraints excluded: chain H residue 2463 LEU Chi-restraints excluded: chain H residue 2471 LEU Chi-restraints excluded: chain H residue 2487 VAL Chi-restraints excluded: chain H residue 2501 ILE Chi-restraints excluded: chain H residue 2505 LYS Chi-restraints excluded: chain H residue 2519 VAL Chi-restraints excluded: chain H residue 2525 LEU Chi-restraints excluded: chain H residue 2554 SER Chi-restraints excluded: chain H residue 2565 ILE Chi-restraints excluded: chain H residue 2603 ILE Chi-restraints excluded: chain H residue 2630 ILE Chi-restraints excluded: chain H residue 2676 VAL Chi-restraints excluded: chain H residue 2693 ILE Chi-restraints excluded: chain H residue 2763 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.042357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.030361 restraints weight = 383220.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.031041 restraints weight = 221596.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.031517 restraints weight = 150540.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.031826 restraints weight = 114119.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.032002 restraints weight = 94663.524| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.6480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.125 34164 Z= 0.489 Angle : 0.974 16.303 46840 Z= 0.502 Chirality : 0.047 0.405 5844 Planarity : 0.006 0.106 6088 Dihedral : 6.534 62.962 5338 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 16.06 % Favored : 83.83 % Rotamer: Outliers : 6.19 % Allowed : 21.59 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.29 % 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: -2.89 (0.13), residues: 3506 helix: -1.12 (0.10), residues: 2270 sheet: -3.94 (0.56), residues: 46 loop : -3.29 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F2613 TYR 0.023 0.003 TYR F2780 PHE 0.026 0.003 PHE F1576 TRP 0.034 0.003 TRP F1805 HIS 0.009 0.002 HIS H1525 Details of bonding type rmsd/Z covalent geometry : bond 0.00992 / 0.49 (34164) covalent geometry : angle 0.97353 / 0.50 (46840) hydrogen bonds : bond 0.04684 / 2.57 ( 2080) hydrogen bonds : angle 5.67085 / 3.04 ( 6132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 94 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1704 MET cc_start: 0.9124 (mmm) cc_final: 0.8899 (mmm) REVERT: F 1711 MET cc_start: 0.9093 (tmm) cc_final: 0.8866 (ppp) REVERT: F 1780 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8649 (t80) REVERT: F 1920 MET cc_start: 0.9320 (mpp) cc_final: 0.8848 (mpp) REVERT: F 1946 LEU cc_start: 0.9562 (tt) cc_final: 0.9147 (tt) REVERT: F 1950 MET cc_start: 0.9009 (mmm) cc_final: 0.8735 (mmm) REVERT: F 2070 MET cc_start: 0.9351 (mmt) cc_final: 0.9092 (mmm) REVERT: F 2155 LYS cc_start: 0.9780 (OUTLIER) cc_final: 0.9543 (ptmm) REVERT: F 2298 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8179 (tp-100) REVERT: F 2372 MET cc_start: 0.9237 (mmm) cc_final: 0.8760 (mmm) REVERT: F 2471 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9049 (mp) REVERT: F 2477 MET cc_start: 0.9376 (tpp) cc_final: 0.9014 (tpp) REVERT: F 2505 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8820 (mtmm) REVERT: F 2704 MET cc_start: 0.8164 (tpp) cc_final: 0.7910 (tpt) REVERT: F 2753 MET cc_start: 0.8446 (mpp) cc_final: 0.8221 (mpp) REVERT: H 1530 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.8191 (m-70) REVERT: H 1711 MET cc_start: 0.9102 (tmm) cc_final: 0.8875 (ppp) REVERT: H 1780 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8591 (t80) REVERT: H 1920 MET cc_start: 0.9306 (mpp) cc_final: 0.8832 (mpp) REVERT: H 1946 LEU cc_start: 0.9565 (tt) cc_final: 0.9153 (tt) REVERT: H 1950 MET cc_start: 0.9022 (mmm) cc_final: 0.8747 (mmm) REVERT: H 2070 MET cc_start: 0.9348 (mmt) cc_final: 0.9094 (mmm) REVERT: H 2155 LYS cc_start: 0.9778 (OUTLIER) cc_final: 0.9539 (ptmm) REVERT: H 2205 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9303 (mt) REVERT: H 2471 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9045 (mp) REVERT: H 2477 MET cc_start: 0.9381 (tpp) cc_final: 0.8995 (tpp) REVERT: H 2505 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8821 (mtmm) REVERT: H 2704 MET cc_start: 0.8709 (ttm) cc_final: 0.8019 (tpt) REVERT: H 2753 MET cc_start: 0.8723 (mpp) cc_final: 0.8372 (mpp) outliers start: 140 outliers final: 121 residues processed: 232 average time/residue: 0.1658 time to fit residues: 68.4415 Evaluate side-chains 226 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 94 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1192 ILE Chi-restraints excluded: chain F residue 1259 LEU Chi-restraints excluded: chain F residue 1284 PHE Chi-restraints excluded: chain F residue 1300 THR Chi-restraints excluded: chain F residue 1350 THR Chi-restraints excluded: chain F residue 1351 ILE Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1408 THR Chi-restraints excluded: chain F residue 1440 ASP Chi-restraints excluded: chain F residue 1460 ILE Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1502 VAL Chi-restraints excluded: chain F residue 1522 VAL Chi-restraints excluded: chain F residue 1530 HIS Chi-restraints excluded: chain F residue 1615 THR Chi-restraints excluded: chain F residue 1649 TYR Chi-restraints excluded: chain F residue 1691 MET Chi-restraints excluded: chain F residue 1694 HIS Chi-restraints excluded: chain F residue 1730 LEU Chi-restraints excluded: chain F residue 1740 LEU Chi-restraints excluded: chain F residue 1771 ILE Chi-restraints excluded: chain F residue 1780 PHE Chi-restraints excluded: chain F residue 1804 THR Chi-restraints excluded: chain F residue 1815 PHE Chi-restraints excluded: chain F residue 1856 VAL Chi-restraints excluded: chain F residue 1865 ASP Chi-restraints excluded: chain F residue 1892 VAL Chi-restraints excluded: chain F residue 1903 LEU Chi-restraints excluded: chain F residue 1922 THR Chi-restraints excluded: chain F residue 1966 LYS Chi-restraints excluded: chain F residue 1967 THR Chi-restraints excluded: chain F residue 1968 THR Chi-restraints excluded: chain F residue 1999 ILE Chi-restraints excluded: chain F residue 2006 VAL Chi-restraints excluded: chain F residue 2048 LEU Chi-restraints excluded: chain F residue 2089 ASP Chi-restraints excluded: chain F residue 2105 LEU Chi-restraints excluded: chain F residue 2108 TRP Chi-restraints excluded: chain F residue 2114 LEU Chi-restraints excluded: chain F residue 2129 ASP Chi-restraints excluded: chain F residue 2155 LYS Chi-restraints excluded: chain F residue 2213 VAL Chi-restraints excluded: chain F residue 2242 TYR Chi-restraints excluded: chain F residue 2268 TYR Chi-restraints excluded: chain F residue 2280 LEU Chi-restraints excluded: chain F residue 2284 ASN Chi-restraints excluded: chain F residue 2298 GLN Chi-restraints excluded: chain F residue 2301 LEU Chi-restraints excluded: chain F residue 2317 LEU Chi-restraints excluded: chain F residue 2345 LYS Chi-restraints excluded: chain F residue 2449 ILE Chi-restraints excluded: chain F residue 2451 THR Chi-restraints excluded: chain F residue 2454 ILE Chi-restraints excluded: chain F residue 2463 LEU Chi-restraints excluded: chain F residue 2471 LEU Chi-restraints excluded: chain F residue 2487 VAL Chi-restraints excluded: chain F residue 2505 LYS Chi-restraints excluded: chain F residue 2519 VAL Chi-restraints excluded: chain F residue 2536 ASP Chi-restraints excluded: chain F residue 2554 SER Chi-restraints excluded: chain F residue 2565 ILE Chi-restraints excluded: chain F residue 2603 ILE Chi-restraints excluded: chain F residue 2630 ILE Chi-restraints excluded: chain F residue 2676 VAL Chi-restraints excluded: chain F residue 2693 ILE Chi-restraints excluded: chain F residue 2763 VAL Chi-restraints excluded: chain H residue 1192 ILE Chi-restraints excluded: chain H residue 1259 LEU Chi-restraints excluded: chain H residue 1284 PHE Chi-restraints excluded: chain H residue 1300 THR Chi-restraints excluded: chain H residue 1350 THR Chi-restraints excluded: chain H residue 1351 ILE Chi-restraints excluded: chain H residue 1397 LEU Chi-restraints excluded: chain H residue 1408 THR Chi-restraints excluded: chain H residue 1440 ASP Chi-restraints excluded: chain H residue 1460 ILE Chi-restraints excluded: chain H residue 1464 LEU Chi-restraints excluded: chain H residue 1502 VAL Chi-restraints excluded: chain H residue 1522 VAL Chi-restraints excluded: chain H residue 1530 HIS Chi-restraints excluded: chain H residue 1649 TYR Chi-restraints excluded: chain H residue 1691 MET Chi-restraints excluded: chain H residue 1694 HIS Chi-restraints excluded: chain H residue 1730 LEU Chi-restraints excluded: chain H residue 1740 LEU Chi-restraints excluded: chain H residue 1771 ILE Chi-restraints excluded: chain H residue 1780 PHE Chi-restraints excluded: chain H residue 1804 THR Chi-restraints excluded: chain H residue 1856 VAL Chi-restraints excluded: chain H residue 1865 ASP Chi-restraints excluded: chain H residue 1892 VAL Chi-restraints excluded: chain H residue 1903 LEU Chi-restraints excluded: chain H residue 1922 THR Chi-restraints excluded: chain H residue 1966 LYS Chi-restraints excluded: chain H residue 1967 THR Chi-restraints excluded: chain H residue 1999 ILE Chi-restraints excluded: chain H residue 2006 VAL Chi-restraints excluded: chain H residue 2048 LEU Chi-restraints excluded: chain H residue 2089 ASP Chi-restraints excluded: chain H residue 2105 LEU Chi-restraints excluded: chain H residue 2108 TRP Chi-restraints excluded: chain H residue 2114 LEU Chi-restraints excluded: chain H residue 2129 ASP Chi-restraints excluded: chain H residue 2155 LYS Chi-restraints excluded: chain H residue 2205 LEU Chi-restraints excluded: chain H residue 2213 VAL Chi-restraints excluded: chain H residue 2242 TYR Chi-restraints excluded: chain H residue 2268 TYR Chi-restraints excluded: chain H residue 2280 LEU Chi-restraints excluded: chain H residue 2284 ASN Chi-restraints excluded: chain H residue 2301 LEU Chi-restraints excluded: chain H residue 2317 LEU Chi-restraints excluded: chain H residue 2345 LYS Chi-restraints excluded: chain H residue 2390 LEU Chi-restraints excluded: chain H residue 2435 GLU Chi-restraints excluded: chain H residue 2449 ILE Chi-restraints excluded: chain H residue 2451 THR Chi-restraints excluded: chain H residue 2454 ILE Chi-restraints excluded: chain H residue 2463 LEU Chi-restraints excluded: chain H residue 2471 LEU Chi-restraints excluded: chain H residue 2487 VAL Chi-restraints excluded: chain H residue 2501 ILE Chi-restraints excluded: chain H residue 2505 LYS Chi-restraints excluded: chain H residue 2519 VAL Chi-restraints excluded: chain H residue 2525 LEU Chi-restraints excluded: chain H residue 2554 SER Chi-restraints excluded: chain H residue 2565 ILE Chi-restraints excluded: chain H residue 2603 ILE Chi-restraints excluded: chain H residue 2630 ILE Chi-restraints excluded: chain H residue 2676 VAL Chi-restraints excluded: chain H residue 2693 ILE Chi-restraints excluded: chain H residue 2763 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.042340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.030331 restraints weight = 379809.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.031009 restraints weight = 220900.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.031466 restraints weight = 150476.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.031688 restraints weight = 115019.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.031954 restraints weight = 98995.607| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.122 34164 Z= 0.488 Angle : 0.976 16.436 46840 Z= 0.503 Chirality : 0.047 0.402 5844 Planarity : 0.006 0.106 6088 Dihedral : 6.549 62.536 5338 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 16.37 % Favored : 83.51 % Rotamer: Outliers : 6.55 % Allowed : 21.33 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.32 % 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: -2.93 (0.13), residues: 3506 helix: -1.16 (0.10), residues: 2272 sheet: -4.06 (0.55), residues: 46 loop : -3.30 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H2307 TYR 0.021 0.003 TYR F1244 PHE 0.025 0.003 PHE F1576 TRP 0.035 0.003 TRP F1805 HIS 0.010 0.002 HIS F1525 Details of bonding type rmsd/Z covalent geometry : bond 0.00990 / 0.49 (34164) covalent geometry : angle 0.97567 / 0.50 (46840) hydrogen bonds : bond 0.04713 / 2.58 ( 2080) hydrogen bonds : angle 5.69966 / 3.05 ( 6132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5710.92 seconds wall clock time: 99 minutes 11.12 seconds (5951.12 seconds total)