Starting phenix.real_space_refine on Thu Jul 31 05:27:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xe4_33154/07_2025/7xe4_33154.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xe4_33154/07_2025/7xe4_33154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xe4_33154/07_2025/7xe4_33154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xe4_33154/07_2025/7xe4_33154.map" model { file = "/net/cci-nas-00/data/ceres_data/7xe4_33154/07_2025/7xe4_33154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xe4_33154/07_2025/7xe4_33154.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 74 5.16 5 C 8258 2.51 5 N 2051 2.21 5 O 2145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12529 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 12246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1503, 12246 Classifications: {'peptide': 1503} Link IDs: {'PTRANS': 65, 'TRANS': 1437} Chain breaks: 10 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 255 Unusual residues: {'C14': 1, 'D10': 6, 'D12': 3, 'DD9': 7, 'HP6': 7, 'XKP': 1} Classifications: {'undetermined': 25} Link IDs: {None: 24} Time building chain proxies: 8.21, per 1000 atoms: 0.66 Number of scatterers: 12529 At special positions: 0 Unit cell: (113.16, 119.6, 129.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 1 15.00 O 2145 8.00 N 2051 7.00 C 8258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 658 " - pdb=" SG CYS F 669 " distance=2.22 Simple disulfide: pdb=" SG CYS F1328 " - pdb=" SG CYS F1345 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F1849 " Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.7 seconds 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 3 sheets defined 61.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 178 through 197 removed outlier: 3.546A pdb=" N MET F 182 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.947A pdb=" N LEU F 206 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 230 removed outlier: 3.766A pdb=" N LYS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 230 " --> pdb=" O PHE F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 243 removed outlier: 4.006A pdb=" N ILE F 236 " --> pdb=" O MET F 232 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 294 removed outlier: 3.536A pdb=" N MET F 293 " --> pdb=" O TRP F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 315 removed outlier: 3.720A pdb=" N ARG F 301 " --> pdb=" O SER F 297 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG F 303 " --> pdb=" O LEU F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 337 removed outlier: 3.832A pdb=" N LEU F 325 " --> pdb=" O THR F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 366 Processing helix chain 'F' and resid 389 through 395 removed outlier: 3.594A pdb=" N GLN F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 399 through 404 Processing helix chain 'F' and resid 413 through 417 Processing helix chain 'F' and resid 419 through 428 removed outlier: 4.093A pdb=" N TYR F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU F 424 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG F 425 " --> pdb=" O ARG F 422 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY F 427 " --> pdb=" O LEU F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 445 No H-bonds generated for 'chain 'F' and resid 443 through 445' Processing helix chain 'F' and resid 446 through 451 removed outlier: 4.246A pdb=" N THR F 450 " --> pdb=" O LEU F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 470 removed outlier: 3.945A pdb=" N TRP F 456 " --> pdb=" O PHE F 452 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL F 457 " --> pdb=" O ASN F 453 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET F 458 " --> pdb=" O ARG F 454 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE F 462 " --> pdb=" O MET F 458 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE F 467 " --> pdb=" O PHE F 463 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN F 470 " --> pdb=" O TYR F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 499 removed outlier: 4.109A pdb=" N TRP F 493 " --> pdb=" O ALA F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 515 removed outlier: 4.552A pdb=" N SER F 504 " --> pdb=" O GLY F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 543 removed outlier: 3.875A pdb=" N SER F 529 " --> pdb=" O ALA F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 551 removed outlier: 4.279A pdb=" N PHE F 548 " --> pdb=" O GLY F 544 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA F 551 " --> pdb=" O ILE F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 561 Processing helix chain 'F' and resid 562 through 582 removed outlier: 3.630A pdb=" N ILE F 582 " --> pdb=" O ILE F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 636 removed outlier: 4.021A pdb=" N PHE F 629 " --> pdb=" O TRP F 625 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR F 633 " --> pdb=" O PHE F 629 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER F 634 " --> pdb=" O ALA F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 644 through 651 removed outlier: 3.813A pdb=" N ILE F 648 " --> pdb=" O LEU F 644 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG F 649 " --> pdb=" O ARG F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 686 removed outlier: 3.823A pdb=" N ILE F 686 " --> pdb=" O ALA F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 711 removed outlier: 3.687A pdb=" N LEU F 690 " --> pdb=" O ILE F 686 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR F 692 " --> pdb=" O PHE F 688 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR F 693 " --> pdb=" O PHE F 689 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 698 " --> pdb=" O LEU F 694 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN F 700 " --> pdb=" O TYR F 696 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU F 711 " --> pdb=" O LYS F 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 726 through 734 removed outlier: 3.753A pdb=" N SER F 732 " --> pdb=" O LYS F 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 764 removed outlier: 3.520A pdb=" N VAL F 753 " --> pdb=" O LEU F 749 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA F 756 " --> pdb=" O GLN F 752 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 758 " --> pdb=" O TRP F 754 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET F 761 " --> pdb=" O ILE F 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 768 through 773 removed outlier: 4.149A pdb=" N GLN F 773 " --> pdb=" O ILE F 769 " (cutoff:3.500A) Processing helix chain 'F' and resid 793 through 797 Processing helix chain 'F' and resid 809 through 812 removed outlier: 3.825A pdb=" N ASP F 812 " --> pdb=" O PHE F 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 809 through 812' Processing helix chain 'F' and resid 813 through 825 removed outlier: 3.718A pdb=" N ARG F 817 " --> pdb=" O SER F 813 " (cutoff:3.500A) Processing helix chain 'F' and resid 857 through 861 removed outlier: 3.907A pdb=" N ILE F 861 " --> pdb=" O ARG F 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 871 through 880 Processing helix chain 'F' and resid 882 through 896 Processing helix chain 'F' and resid 933 through 946 removed outlier: 3.628A pdb=" N ARG F 946 " --> pdb=" O TRP F 942 " (cutoff:3.500A) Processing helix chain 'F' and resid 950 through 958 Processing helix chain 'F' and resid 958 through 972 removed outlier: 3.967A pdb=" N ARG F 962 " --> pdb=" O MET F 958 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN F 972 " --> pdb=" O TYR F 968 " (cutoff:3.500A) Processing helix chain 'F' and resid 973 through 978 removed outlier: 3.829A pdb=" N GLN F 977 " --> pdb=" O PRO F 973 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET F 978 " --> pdb=" O GLU F 974 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 973 through 978' Processing helix chain 'F' and resid 982 through 995 Processing helix chain 'F' and resid 1006 through 1010 removed outlier: 3.799A pdb=" N PHE F1010 " --> pdb=" O LEU F1007 " (cutoff:3.500A) Processing helix chain 'F' and resid 1011 through 1025 removed outlier: 3.921A pdb=" N GLU F1016 " --> pdb=" O PRO F1012 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASN F1017 " --> pdb=" O HIS F1013 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F1018 " --> pdb=" O GLU F1014 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU F1022 " --> pdb=" O ALA F1018 " (cutoff:3.500A) Processing helix chain 'F' and resid 1083 through 1088 removed outlier: 3.652A pdb=" N ASN F1087 " --> pdb=" O SER F1083 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS F1088 " --> pdb=" O ASP F1084 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1083 through 1088' Processing helix chain 'F' and resid 1114 through 1119 removed outlier: 3.894A pdb=" N VAL F1118 " --> pdb=" O LYS F1114 " (cutoff:3.500A) Processing helix chain 'F' and resid 1169 through 1187 removed outlier: 3.633A pdb=" N GLN F1186 " --> pdb=" O ARG F1182 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE F1187 " --> pdb=" O THR F1183 " (cutoff:3.500A) Processing helix chain 'F' and resid 1201 through 1207 removed outlier: 3.815A pdb=" N THR F1206 " --> pdb=" O THR F1202 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG F1207 " --> pdb=" O PHE F1203 " (cutoff:3.500A) Processing helix chain 'F' and resid 1223 through 1231 Processing helix chain 'F' and resid 1273 through 1282 removed outlier: 3.581A pdb=" N THR F1280 " --> pdb=" O TYR F1276 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN F1281 " --> pdb=" O TYR F1277 " (cutoff:3.500A) Processing helix chain 'F' and resid 1283 through 1292 removed outlier: 3.812A pdb=" N THR F1289 " --> pdb=" O ASP F1285 " (cutoff:3.500A) Processing helix chain 'F' and resid 1294 through 1299 removed outlier: 4.129A pdb=" N HIS F1298 " --> pdb=" O HIS F1294 " (cutoff:3.500A) Processing helix chain 'F' and resid 1299 through 1323 removed outlier: 3.973A pdb=" N PHE F1303 " --> pdb=" O LEU F1299 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN F1305 " --> pdb=" O ASN F1301 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN F1309 " --> pdb=" O GLN F1305 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR F1314 " --> pdb=" O MET F1310 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN F1317 " --> pdb=" O LEU F1313 " (cutoff:3.500A) Processing helix chain 'F' and resid 1348 through 1369 removed outlier: 4.290A pdb=" N VAL F1355 " --> pdb=" O ALA F1351 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG F1356 " --> pdb=" O VAL F1352 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG F1357 " --> pdb=" O ASP F1353 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F1360 " --> pdb=" O ARG F1356 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER F1361 " --> pdb=" O ARG F1357 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F1364 " --> pdb=" O LEU F1360 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL F1365 " --> pdb=" O SER F1361 " (cutoff:3.500A) Processing helix chain 'F' and resid 1371 through 1379 removed outlier: 4.023A pdb=" N VAL F1375 " --> pdb=" O VAL F1371 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN F1376 " --> pdb=" O PRO F1372 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F1377 " --> pdb=" O ILE F1373 " (cutoff:3.500A) Processing helix chain 'F' and resid 1382 through 1392 removed outlier: 3.893A pdb=" N GLN F1388 " --> pdb=" O TRP F1384 " (cutoff:3.500A) Processing helix chain 'F' and resid 1398 through 1406 Processing helix chain 'F' and resid 1408 through 1418 Processing helix chain 'F' and resid 1437 through 1445 removed outlier: 3.654A pdb=" N LEU F1441 " --> pdb=" O PRO F1437 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG F1444 " --> pdb=" O ILE F1440 " (cutoff:3.500A) Processing helix chain 'F' and resid 1450 through 1467 Processing helix chain 'F' and resid 1469 through 1471 No H-bonds generated for 'chain 'F' and resid 1469 through 1471' Processing helix chain 'F' and resid 1472 through 1483 removed outlier: 3.874A pdb=" N TRP F1476 " --> pdb=" O LEU F1472 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER F1478 " --> pdb=" O TRP F1474 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE F1483 " --> pdb=" O LEU F1479 " (cutoff:3.500A) Processing helix chain 'F' and resid 1496 through 1512 removed outlier: 3.628A pdb=" N PHE F1500 " --> pdb=" O TRP F1496 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP F1505 " --> pdb=" O LEU F1501 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F1507 " --> pdb=" O TYR F1503 " (cutoff:3.500A) Processing helix chain 'F' and resid 1559 through 1564 removed outlier: 3.866A pdb=" N GLU F1564 " --> pdb=" O LEU F1560 " (cutoff:3.500A) Processing helix chain 'F' and resid 1565 through 1584 removed outlier: 5.779A pdb=" N TYR F1571 " --> pdb=" O PRO F1567 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA F1572 " --> pdb=" O CYS F1568 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS F1575 " --> pdb=" O TYR F1571 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA F1578 " --> pdb=" O GLY F1574 " (cutoff:3.500A) Processing helix chain 'F' and resid 1598 through 1607 removed outlier: 3.889A pdb=" N ILE F1602 " --> pdb=" O SER F1598 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F1603 " --> pdb=" O VAL F1599 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS F1605 " --> pdb=" O ARG F1601 " (cutoff:3.500A) Processing helix chain 'F' and resid 1607 through 1626 removed outlier: 3.594A pdb=" N SER F1624 " --> pdb=" O CYS F1620 " (cutoff:3.500A) Processing helix chain 'F' and resid 1639 through 1665 removed outlier: 3.911A pdb=" N ILE F1652 " --> pdb=" O GLY F1648 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N HIS F1654 " --> pdb=" O ALA F1650 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP F1662 " --> pdb=" O PHE F1658 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU F1665 " --> pdb=" O MET F1661 " (cutoff:3.500A) Processing helix chain 'F' and resid 1669 through 1697 removed outlier: 4.348A pdb=" N ILE F1674 " --> pdb=" O VAL F1670 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY F1675 " --> pdb=" O ARG F1671 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA F1692 " --> pdb=" O HIS F1688 " (cutoff:3.500A) Processing helix chain 'F' and resid 1725 through 1751 removed outlier: 3.667A pdb=" N LEU F1730 " --> pdb=" O PRO F1726 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F1733 " --> pdb=" O GLU F1729 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F1742 " --> pdb=" O SER F1738 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE F1750 " --> pdb=" O LEU F1746 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU F1751 " --> pdb=" O GLY F1747 " (cutoff:3.500A) Processing helix chain 'F' and resid 1754 through 1759 removed outlier: 3.700A pdb=" N ILE F1759 " --> pdb=" O LEU F1755 " (cutoff:3.500A) Processing helix chain 'F' and resid 1763 through 1775 removed outlier: 3.527A pdb=" N LEU F1774 " --> pdb=" O MET F1770 " (cutoff:3.500A) Processing helix chain 'F' and resid 1786 through 1821 removed outlier: 3.522A pdb=" N LYS F1799 " --> pdb=" O ARG F1795 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR F1800 " --> pdb=" O MET F1796 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER F1802 " --> pdb=" O LYS F1798 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F1803 " --> pdb=" O LYS F1799 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE F1805 " --> pdb=" O CYS F1801 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F1815 " --> pdb=" O PHE F1811 " (cutoff:3.500A) Proline residue: F1818 - end of helix Processing helix chain 'F' and resid 1822 through 1824 No H-bonds generated for 'chain 'F' and resid 1822 through 1824' Processing sheet with id=AA1, first strand: chain 'F' and resid 371 through 372 Processing sheet with id=AA2, first strand: chain 'F' and resid 779 through 781 Processing sheet with id=AA3, first strand: chain 'F' and resid 1068 through 1071 removed outlier: 4.195A pdb=" N PHE F1068 " --> pdb=" O LEU F1051 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU F1051 " --> pdb=" O PHE F1068 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU F1033 " --> pdb=" O MET F1004 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE F 842 " --> pdb=" O LYS F 999 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU F1001 " --> pdb=" O PHE F 842 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL F 844 " --> pdb=" O LEU F1001 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER F1003 " --> pdb=" O VAL F 844 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR F 846 " --> pdb=" O SER F1003 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR F 843 " --> pdb=" O GLN F1099 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE F1150 " --> pdb=" O LYS F1237 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1545 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: 5.26 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2098 1.32 - 1.45: 3484 1.45 - 1.57: 7130 1.57 - 1.69: 2 1.69 - 1.82: 118 Bond restraints: 12832 Sorted by residual: bond pdb=" C17 XKP F1925 " pdb=" C22 XKP F1925 " ideal model delta sigma weight residual 1.524 1.306 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C SER F1398 " pdb=" N PRO F1399 " ideal model delta sigma weight residual 1.335 1.390 -0.054 1.36e-02 5.41e+03 1.60e+01 bond pdb=" C GLN F1842 " pdb=" N PRO F1843 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.22e-02 6.72e+03 5.66e+00 bond pdb=" C8 XKP F1925 " pdb=" O2 XKP F1925 " ideal model delta sigma weight residual 1.409 1.452 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" N ILE F 455 " pdb=" CA ILE F 455 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.32e-02 5.74e+03 4.42e+00 ... (remaining 12827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 16781 2.26 - 4.52: 454 4.52 - 6.78: 59 6.78 - 9.04: 7 9.04 - 11.30: 3 Bond angle restraints: 17304 Sorted by residual: angle pdb=" N VAL F 882 " pdb=" CA VAL F 882 " pdb=" C VAL F 882 " ideal model delta sigma weight residual 113.71 107.39 6.32 9.50e-01 1.11e+00 4.43e+01 angle pdb=" N ILE F1844 " pdb=" CA ILE F1844 " pdb=" C ILE F1844 " ideal model delta sigma weight residual 113.71 107.97 5.74 9.50e-01 1.11e+00 3.65e+01 angle pdb=" C ASN F 280 " pdb=" CA ASN F 280 " pdb=" CB ASN F 280 " ideal model delta sigma weight residual 116.54 110.67 5.87 1.15e+00 7.56e-01 2.61e+01 angle pdb=" C ASP F 231 " pdb=" CA ASP F 231 " pdb=" CB ASP F 231 " ideal model delta sigma weight residual 117.23 110.35 6.88 1.36e+00 5.41e-01 2.56e+01 angle pdb=" N LEU F1757 " pdb=" CA LEU F1757 " pdb=" C LEU F1757 " ideal model delta sigma weight residual 114.75 108.67 6.08 1.26e+00 6.30e-01 2.33e+01 ... (remaining 17299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.78: 7323 28.78 - 57.57: 280 57.57 - 86.35: 24 86.35 - 115.14: 2 115.14 - 143.92: 7 Dihedral angle restraints: 7636 sinusoidal: 3217 harmonic: 4419 Sorted by residual: dihedral pdb=" CB CYS F1328 " pdb=" SG CYS F1328 " pdb=" SG CYS F1345 " pdb=" CB CYS F1345 " ideal model delta sinusoidal sigma weight residual 93.00 146.31 -53.31 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA LEU F1840 " pdb=" C LEU F1840 " pdb=" N PHE F1841 " pdb=" CA PHE F1841 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" C6 XKP F1925 " pdb=" C7 XKP F1925 " pdb=" C8 XKP F1925 " pdb=" O2 XKP F1925 " ideal model delta sinusoidal sigma weight residual -67.90 76.02 -143.92 1 3.00e+01 1.11e-03 1.93e+01 ... (remaining 7633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1669 0.067 - 0.133: 212 0.133 - 0.200: 10 0.200 - 0.267: 1 0.267 - 0.333: 1 Chirality restraints: 1893 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.73 0.33 2.00e-02 2.50e+03 2.78e+02 chirality pdb=" C7 XKP F1925 " pdb=" C6 XKP F1925 " pdb=" C8 XKP F1925 " pdb=" O6 XKP F1925 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA THR F 438 " pdb=" N THR F 438 " pdb=" C THR F 438 " pdb=" CB THR F 438 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 1890 not shown) Planarity restraints: 2143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F1849 " 0.102 2.00e-02 2.50e+03 9.87e-02 1.22e+02 pdb=" CG ASN F1849 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN F1849 " -0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN F1849 " -0.131 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.064 2.00e-02 2.50e+03 5.28e-02 3.48e+01 pdb=" C7 NAG A 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.049 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.083 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 699 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C VAL F 699 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL F 699 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN F 700 " 0.017 2.00e-02 2.50e+03 ... (remaining 2140 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1266 2.74 - 3.28: 12816 3.28 - 3.82: 18609 3.82 - 4.36: 21274 4.36 - 4.90: 36743 Nonbonded interactions: 90708 Sorted by model distance: nonbonded pdb=" NE2 HIS F 771 " pdb=" O GLU F 807 " model vdw 2.199 3.120 nonbonded pdb=" O ARG F 852 " pdb=" OG1 THR F 949 " model vdw 2.200 3.040 nonbonded pdb=" O SER F 751 " pdb=" ND2 ASN F 755 " model vdw 2.204 3.120 nonbonded pdb=" OD1 ASN F1849 " pdb=" O5 NAG A 1 " model vdw 2.211 3.040 nonbonded pdb=" O ARG F1728 " pdb=" OG1 THR F1731 " model vdw 2.225 3.040 ... (remaining 90703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.220 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.006 0.218 12836 Z= 0.297 Angle : 1.049 58.758 17314 Z= 0.570 Chirality : 0.045 0.333 1893 Planarity : 0.005 0.070 2142 Dihedral : 15.211 143.921 4772 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.99 % Favored : 89.60 % Rotamer: Outliers : 0.45 % Allowed : 0.53 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.22), residues: 1481 helix: -0.35 (0.19), residues: 777 sheet: -2.30 (0.69), residues: 54 loop : -3.26 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F1474 HIS 0.004 0.001 HIS F 188 PHE 0.026 0.002 PHE F1658 TYR 0.039 0.002 TYR F 148 ARG 0.010 0.001 ARG F 817 Details of bonding type rmsd link_NAG-ASN : bond 0.17814 ( 1) link_NAG-ASN : angle 15.54178 ( 3) link_BETA1-4 : bond 0.04201 ( 1) link_BETA1-4 : angle 16.98257 ( 3) hydrogen bonds : bond 0.27789 ( 528) hydrogen bonds : angle 7.29999 ( 1545) SS BOND : bond 0.13041 ( 2) SS BOND : angle 34.13197 ( 4) covalent geometry : bond 0.00573 (12832) covalent geometry : angle 0.86061 (17304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 709 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.5914 (t80) REVERT: F 774 LYS cc_start: 0.8980 (pttt) cc_final: 0.8681 (ttpt) REVERT: F 878 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8836 (tm-30) REVERT: F 1400 MET cc_start: 0.2644 (tmm) cc_final: 0.1041 (ptp) outliers start: 6 outliers final: 2 residues processed: 177 average time/residue: 0.2612 time to fit residues: 67.6447 Evaluate side-chains 142 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 669 CYS Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 709 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 0.0170 chunk 136 optimal weight: 30.0000 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1220 ASN F1854 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081418 restraints weight = 26464.022| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.62 r_work: 0.2911 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12836 Z= 0.172 Angle : 0.701 9.871 17314 Z= 0.363 Chirality : 0.044 0.229 1893 Planarity : 0.005 0.066 2142 Dihedral : 9.747 135.125 1886 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.86 % Favored : 89.94 % Rotamer: Outliers : 0.76 % Allowed : 8.03 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.22), residues: 1481 helix: 0.12 (0.18), residues: 819 sheet: -2.18 (0.71), residues: 54 loop : -3.23 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F1474 HIS 0.005 0.001 HIS F 765 PHE 0.021 0.002 PHE F1658 TYR 0.027 0.002 TYR F 148 ARG 0.005 0.001 ARG F 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 1) link_NAG-ASN : angle 4.08502 ( 3) link_BETA1-4 : bond 0.00885 ( 1) link_BETA1-4 : angle 5.83676 ( 3) hydrogen bonds : bond 0.07110 ( 528) hydrogen bonds : angle 4.82499 ( 1545) SS BOND : bond 0.01160 ( 2) SS BOND : angle 0.71991 ( 4) covalent geometry : bond 0.00365 (12832) covalent geometry : angle 0.69459 (17304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 1.436 Fit side-chains REVERT: F 386 LYS cc_start: 0.9087 (mttm) cc_final: 0.8681 (mttm) REVERT: F 774 LYS cc_start: 0.9093 (pttt) cc_final: 0.8822 (pttt) REVERT: F 878 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8886 (tm-30) REVERT: F 884 TRP cc_start: 0.9214 (t-100) cc_final: 0.8770 (t-100) REVERT: F 1053 ASP cc_start: 0.8879 (t70) cc_final: 0.8613 (t70) REVERT: F 1220 ASN cc_start: 0.7390 (t160) cc_final: 0.6947 (m-40) REVERT: F 1499 PHE cc_start: 0.8786 (t80) cc_final: 0.8540 (t80) REVERT: F 1672 MET cc_start: 0.9109 (tmm) cc_final: 0.8749 (tmm) REVERT: F 1736 GLU cc_start: 0.9126 (tp30) cc_final: 0.8833 (tp30) REVERT: F 1796 MET cc_start: 0.8258 (tpt) cc_final: 0.7613 (tpt) REVERT: F 1842 GLN cc_start: 0.7342 (tm-30) cc_final: 0.7095 (tm-30) outliers start: 10 outliers final: 4 residues processed: 170 average time/residue: 0.3041 time to fit residues: 77.0985 Evaluate side-chains 145 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 935 TYR Chi-restraints excluded: chain F residue 1806 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 142 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 0.0870 chunk 139 optimal weight: 8.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 ASN ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.122726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.081299 restraints weight = 26652.115| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.66 r_work: 0.2895 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12836 Z= 0.167 Angle : 0.644 9.117 17314 Z= 0.332 Chirality : 0.042 0.223 1893 Planarity : 0.005 0.073 2142 Dihedral : 8.952 155.415 1879 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.25 % Favored : 90.55 % Rotamer: Outliers : 1.67 % Allowed : 12.50 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.22), residues: 1481 helix: 0.37 (0.19), residues: 831 sheet: -1.98 (0.72), residues: 54 loop : -3.24 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F1474 HIS 0.005 0.001 HIS F 765 PHE 0.015 0.001 PHE F1499 TYR 0.023 0.001 TYR F 148 ARG 0.004 0.000 ARG F 817 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 1) link_NAG-ASN : angle 3.42060 ( 3) link_BETA1-4 : bond 0.00037 ( 1) link_BETA1-4 : angle 5.91684 ( 3) hydrogen bonds : bond 0.06199 ( 528) hydrogen bonds : angle 4.41252 ( 1545) SS BOND : bond 0.00976 ( 2) SS BOND : angle 1.97856 ( 4) covalent geometry : bond 0.00371 (12832) covalent geometry : angle 0.63734 (17304) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 2.139 Fit side-chains REVERT: F 230 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8678 (pp) REVERT: F 317 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8422 (tm-30) REVERT: F 774 LYS cc_start: 0.9100 (pttt) cc_final: 0.8834 (pttt) REVERT: F 858 ARG cc_start: 0.8488 (ttp80) cc_final: 0.7978 (ttp80) REVERT: F 878 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8879 (tm-30) REVERT: F 884 TRP cc_start: 0.9244 (t-100) cc_final: 0.8774 (t-100) REVERT: F 1220 ASN cc_start: 0.7353 (t0) cc_final: 0.6920 (m-40) REVERT: F 1400 MET cc_start: 0.2629 (tmm) cc_final: 0.1009 (ptp) REVERT: F 1499 PHE cc_start: 0.8624 (t80) cc_final: 0.8303 (t80) REVERT: F 1503 TYR cc_start: 0.9446 (t80) cc_final: 0.9228 (t80) REVERT: F 1736 GLU cc_start: 0.9048 (tp30) cc_final: 0.8758 (tp30) REVERT: F 1795 ARG cc_start: 0.8593 (tpp-160) cc_final: 0.8388 (tpp-160) REVERT: F 1796 MET cc_start: 0.8524 (tpt) cc_final: 0.8324 (tpt) outliers start: 22 outliers final: 11 residues processed: 167 average time/residue: 0.3263 time to fit residues: 81.0570 Evaluate side-chains 154 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 770 ASP Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 935 TYR Chi-restraints excluded: chain F residue 1224 TYR Chi-restraints excluded: chain F residue 1308 LEU Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1617 LEU Chi-restraints excluded: chain F residue 1797 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 34 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 ASN ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1186 GLN ** 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 = 0.3765 r_free = 0.3765 target = 0.123710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.082197 restraints weight = 26399.031| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.65 r_work: 0.2911 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12836 Z= 0.144 Angle : 0.621 10.209 17314 Z= 0.315 Chirality : 0.042 0.203 1893 Planarity : 0.004 0.070 2142 Dihedral : 8.474 153.786 1879 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.52 % Favored : 90.28 % Rotamer: Outliers : 1.67 % Allowed : 15.38 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1481 helix: 0.69 (0.19), residues: 811 sheet: -1.86 (0.73), residues: 54 loop : -3.10 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F1474 HIS 0.005 0.001 HIS F1647 PHE 0.016 0.001 PHE F1669 TYR 0.020 0.001 TYR F 148 ARG 0.006 0.000 ARG F 817 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 1) link_NAG-ASN : angle 3.09154 ( 3) link_BETA1-4 : bond 0.00043 ( 1) link_BETA1-4 : angle 5.44993 ( 3) hydrogen bonds : bond 0.05292 ( 528) hydrogen bonds : angle 4.13416 ( 1545) SS BOND : bond 0.00642 ( 2) SS BOND : angle 0.97007 ( 4) covalent geometry : bond 0.00320 (12832) covalent geometry : angle 0.61536 (17304) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.311 Fit side-chains REVERT: F 230 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8796 (pp) REVERT: F 317 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: F 774 LYS cc_start: 0.9100 (pttt) cc_final: 0.8821 (pttt) REVERT: F 858 ARG cc_start: 0.8466 (ttp80) cc_final: 0.7881 (ttp80) REVERT: F 862 ARG cc_start: 0.7338 (tmm-80) cc_final: 0.7069 (ttp80) REVERT: F 884 TRP cc_start: 0.9215 (t-100) cc_final: 0.8771 (t-100) REVERT: F 892 LYS cc_start: 0.9391 (pttt) cc_final: 0.9148 (pttm) REVERT: F 1053 ASP cc_start: 0.8669 (t70) cc_final: 0.8423 (t70) REVERT: F 1220 ASN cc_start: 0.7371 (t0) cc_final: 0.6873 (m-40) REVERT: F 1327 MET cc_start: 0.9042 (mpp) cc_final: 0.8826 (mpp) REVERT: F 1499 PHE cc_start: 0.8571 (t80) cc_final: 0.8277 (t80) REVERT: F 1565 ILE cc_start: 0.8124 (mm) cc_final: 0.7879 (mm) REVERT: F 1736 GLU cc_start: 0.9002 (tp30) cc_final: 0.8703 (tp30) REVERT: F 1791 ARG cc_start: 0.8860 (ptm-80) cc_final: 0.8581 (ptp90) REVERT: F 1795 ARG cc_start: 0.8567 (tpp-160) cc_final: 0.8222 (tpp-160) outliers start: 22 outliers final: 12 residues processed: 172 average time/residue: 0.2504 time to fit residues: 63.1058 Evaluate side-chains 156 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 550 PHE Chi-restraints excluded: chain F residue 770 ASP Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 935 TYR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1224 TYR Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1617 LEU Chi-restraints excluded: chain F residue 1737 LEU Chi-restraints excluded: chain F residue 1806 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 114 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 45 optimal weight: 0.0270 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 ASN ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1668 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.125451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.084232 restraints weight = 26166.750| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.62 r_work: 0.2953 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12836 Z= 0.115 Angle : 0.594 10.360 17314 Z= 0.298 Chirality : 0.040 0.198 1893 Planarity : 0.004 0.074 2142 Dihedral : 7.787 128.703 1879 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.58 % Favored : 91.22 % Rotamer: Outliers : 1.82 % Allowed : 16.52 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1481 helix: 0.85 (0.19), residues: 811 sheet: -1.78 (0.71), residues: 54 loop : -2.93 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F1474 HIS 0.005 0.001 HIS F1647 PHE 0.020 0.001 PHE F 821 TYR 0.016 0.001 TYR F 148 ARG 0.005 0.000 ARG F 938 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 1) link_NAG-ASN : angle 2.98864 ( 3) link_BETA1-4 : bond 0.00077 ( 1) link_BETA1-4 : angle 5.29019 ( 3) hydrogen bonds : bond 0.04535 ( 528) hydrogen bonds : angle 3.89341 ( 1545) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.76103 ( 4) covalent geometry : bond 0.00241 (12832) covalent geometry : angle 0.58873 (17304) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.273 Fit side-chains REVERT: F 230 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8655 (pp) REVERT: F 346 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7307 (tm-30) REVERT: F 658 CYS cc_start: 0.6430 (OUTLIER) cc_final: 0.6080 (p) REVERT: F 774 LYS cc_start: 0.9076 (pttt) cc_final: 0.8796 (pttt) REVERT: F 858 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8144 (ttp80) REVERT: F 884 TRP cc_start: 0.9179 (t-100) cc_final: 0.8791 (t-100) REVERT: F 1220 ASN cc_start: 0.7234 (t0) cc_final: 0.6690 (m-40) REVERT: F 1327 MET cc_start: 0.9049 (mpp) cc_final: 0.8812 (mpp) REVERT: F 1400 MET cc_start: 0.2392 (tmm) cc_final: 0.0624 (ptp) REVERT: F 1565 ILE cc_start: 0.8047 (mm) cc_final: 0.7832 (mm) REVERT: F 1736 GLU cc_start: 0.8979 (tp30) cc_final: 0.8690 (tp30) REVERT: F 1795 ARG cc_start: 0.8564 (tpp-160) cc_final: 0.8272 (tpp-160) outliers start: 24 outliers final: 12 residues processed: 184 average time/residue: 0.2310 time to fit residues: 62.4812 Evaluate side-chains 163 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 550 PHE Chi-restraints excluded: chain F residue 658 CYS Chi-restraints excluded: chain F residue 770 ASP Chi-restraints excluded: chain F residue 879 LEU Chi-restraints excluded: chain F residue 935 TYR Chi-restraints excluded: chain F residue 1127 VAL Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1224 TYR Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 58 optimal weight: 0.2980 chunk 119 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 80 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 ASN F 317 GLN ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN F1186 GLN F1668 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.083973 restraints weight = 25746.052| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.58 r_work: 0.2946 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12836 Z= 0.113 Angle : 0.603 12.379 17314 Z= 0.297 Chirality : 0.040 0.182 1893 Planarity : 0.004 0.069 2142 Dihedral : 7.212 100.799 1879 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.37 % Favored : 91.42 % Rotamer: Outliers : 2.58 % Allowed : 17.50 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1481 helix: 1.09 (0.19), residues: 804 sheet: -1.67 (0.71), residues: 54 loop : -2.88 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F1474 HIS 0.004 0.001 HIS F1647 PHE 0.011 0.001 PHE F1401 TYR 0.015 0.001 TYR F1330 ARG 0.005 0.000 ARG F1791 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 1) link_NAG-ASN : angle 2.82925 ( 3) link_BETA1-4 : bond 0.00019 ( 1) link_BETA1-4 : angle 5.12502 ( 3) hydrogen bonds : bond 0.04189 ( 528) hydrogen bonds : angle 3.74268 ( 1545) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.68895 ( 4) covalent geometry : bond 0.00241 (12832) covalent geometry : angle 0.59837 (17304) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.299 Fit side-chains REVERT: F 658 CYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5944 (p) REVERT: F 774 LYS cc_start: 0.9081 (pttt) cc_final: 0.8813 (pttt) REVERT: F 858 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8116 (ttp80) REVERT: F 1053 ASP cc_start: 0.8649 (t70) cc_final: 0.8364 (t70) REVERT: F 1220 ASN cc_start: 0.7279 (t0) cc_final: 0.6853 (t0) REVERT: F 1327 MET cc_start: 0.9042 (mpp) cc_final: 0.8764 (mpp) REVERT: F 1400 MET cc_start: 0.2368 (tmm) cc_final: 0.0736 (ptp) REVERT: F 1594 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: F 1736 GLU cc_start: 0.8971 (tp30) cc_final: 0.8715 (tp30) REVERT: F 1791 ARG cc_start: 0.8936 (ptm-80) cc_final: 0.8498 (ttm110) REVERT: F 1795 ARG cc_start: 0.8542 (tpp-160) cc_final: 0.8209 (tpp-160) outliers start: 34 outliers final: 17 residues processed: 188 average time/residue: 0.2866 time to fit residues: 79.6029 Evaluate side-chains 168 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 550 PHE Chi-restraints excluded: chain F residue 658 CYS Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 770 ASP Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 839 MET Chi-restraints excluded: chain F residue 879 LEU Chi-restraints excluded: chain F residue 1127 VAL Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1224 TYR Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1594 ASP Chi-restraints excluded: chain F residue 1617 LEU Chi-restraints excluded: chain F residue 1668 ASN Chi-restraints excluded: chain F residue 1797 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 5 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN F1668 ASN ** F1838 HIS ** 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 = 0.3753 r_free = 0.3753 target = 0.124168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.083444 restraints weight = 25716.589| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.56 r_work: 0.2941 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12836 Z= 0.122 Angle : 0.622 12.488 17314 Z= 0.306 Chirality : 0.041 0.280 1893 Planarity : 0.004 0.073 2142 Dihedral : 7.005 87.054 1879 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.37 % Favored : 91.42 % Rotamer: Outliers : 2.20 % Allowed : 18.71 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1481 helix: 1.10 (0.19), residues: 809 sheet: -1.63 (0.71), residues: 54 loop : -2.84 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F1474 HIS 0.006 0.001 HIS F1838 PHE 0.013 0.001 PHE F1499 TYR 0.015 0.001 TYR F1330 ARG 0.003 0.000 ARG F1791 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 1) link_NAG-ASN : angle 2.76223 ( 3) link_BETA1-4 : bond 0.00225 ( 1) link_BETA1-4 : angle 4.98227 ( 3) hydrogen bonds : bond 0.04215 ( 528) hydrogen bonds : angle 3.74298 ( 1545) SS BOND : bond 0.00219 ( 2) SS BOND : angle 0.70303 ( 4) covalent geometry : bond 0.00268 (12832) covalent geometry : angle 0.61796 (17304) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: F 441 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: F 658 CYS cc_start: 0.6287 (OUTLIER) cc_final: 0.5937 (p) REVERT: F 774 LYS cc_start: 0.9085 (pttt) cc_final: 0.8814 (pttt) REVERT: F 858 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8079 (ttp80) REVERT: F 892 LYS cc_start: 0.9363 (pttt) cc_final: 0.9106 (pttp) REVERT: F 1053 ASP cc_start: 0.8629 (t70) cc_final: 0.8342 (t70) REVERT: F 1220 ASN cc_start: 0.7283 (t0) cc_final: 0.6861 (t0) REVERT: F 1327 MET cc_start: 0.9022 (mpp) cc_final: 0.8719 (mpp) REVERT: F 1400 MET cc_start: 0.2475 (tmm) cc_final: 0.0849 (ptp) REVERT: F 1594 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8269 (t70) REVERT: F 1694 MET cc_start: 0.3473 (tpp) cc_final: 0.3219 (ttp) REVERT: F 1736 GLU cc_start: 0.8996 (tp30) cc_final: 0.8653 (tp30) REVERT: F 1739 GLU cc_start: 0.9209 (tt0) cc_final: 0.8809 (tm-30) REVERT: F 1791 ARG cc_start: 0.8947 (ptm-80) cc_final: 0.8504 (ttm110) REVERT: F 1795 ARG cc_start: 0.8579 (tpp-160) cc_final: 0.8193 (tpp-160) outliers start: 29 outliers final: 20 residues processed: 176 average time/residue: 0.4024 time to fit residues: 104.0152 Evaluate side-chains 169 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 441 GLU Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 550 PHE Chi-restraints excluded: chain F residue 658 CYS Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 770 ASP Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 839 MET Chi-restraints excluded: chain F residue 879 LEU Chi-restraints excluded: chain F residue 935 TYR Chi-restraints excluded: chain F residue 1092 PHE Chi-restraints excluded: chain F residue 1127 VAL Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1224 TYR Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1594 ASP Chi-restraints excluded: chain F residue 1617 LEU Chi-restraints excluded: chain F residue 1797 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 25 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 15 optimal weight: 0.0980 chunk 102 optimal weight: 0.4980 chunk 140 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN F1469 GLN F1842 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.125058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083223 restraints weight = 25577.808| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.60 r_work: 0.2912 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12836 Z= 0.117 Angle : 0.613 10.298 17314 Z= 0.303 Chirality : 0.041 0.177 1893 Planarity : 0.004 0.070 2142 Dihedral : 6.646 86.094 1879 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.64 % Favored : 91.15 % Rotamer: Outliers : 1.89 % Allowed : 19.02 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1481 helix: 1.19 (0.19), residues: 809 sheet: -1.57 (0.71), residues: 54 loop : -2.80 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F1474 HIS 0.004 0.001 HIS F1647 PHE 0.022 0.001 PHE F1499 TYR 0.015 0.001 TYR F1330 ARG 0.004 0.000 ARG F1116 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 1) link_NAG-ASN : angle 2.72659 ( 3) link_BETA1-4 : bond 0.00232 ( 1) link_BETA1-4 : angle 4.82557 ( 3) hydrogen bonds : bond 0.04100 ( 528) hydrogen bonds : angle 3.69719 ( 1545) SS BOND : bond 0.00210 ( 2) SS BOND : angle 0.70864 ( 4) covalent geometry : bond 0.00255 (12832) covalent geometry : angle 0.60917 (17304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.400 Fit side-chains REVERT: F 441 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: F 658 CYS cc_start: 0.6259 (OUTLIER) cc_final: 0.5930 (p) REVERT: F 774 LYS cc_start: 0.9131 (pttt) cc_final: 0.8855 (pttt) REVERT: F 858 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8017 (ttp80) REVERT: F 1053 ASP cc_start: 0.8669 (t70) cc_final: 0.8335 (t70) REVERT: F 1220 ASN cc_start: 0.7261 (t0) cc_final: 0.6830 (t0) REVERT: F 1327 MET cc_start: 0.8991 (mpp) cc_final: 0.8682 (mpp) REVERT: F 1400 MET cc_start: 0.2576 (tmm) cc_final: 0.1034 (ptp) REVERT: F 1562 MET cc_start: 0.7728 (tmm) cc_final: 0.7459 (tmm) REVERT: F 1736 GLU cc_start: 0.8966 (tp30) cc_final: 0.8626 (tp30) REVERT: F 1739 GLU cc_start: 0.9238 (tt0) cc_final: 0.8803 (tm-30) REVERT: F 1791 ARG cc_start: 0.8972 (ptm-80) cc_final: 0.8531 (ttm110) REVERT: F 1795 ARG cc_start: 0.8614 (tpp-160) cc_final: 0.8108 (tpp-160) outliers start: 25 outliers final: 15 residues processed: 174 average time/residue: 0.2524 time to fit residues: 64.3465 Evaluate side-chains 168 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 441 GLU Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 658 CYS Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 839 MET Chi-restraints excluded: chain F residue 879 LEU Chi-restraints excluded: chain F residue 1088 HIS Chi-restraints excluded: chain F residue 1092 PHE Chi-restraints excluded: chain F residue 1127 VAL Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1797 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 102 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.124280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.082293 restraints weight = 25544.684| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.60 r_work: 0.2892 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12836 Z= 0.132 Angle : 0.629 13.839 17314 Z= 0.313 Chirality : 0.041 0.175 1893 Planarity : 0.004 0.073 2142 Dihedral : 6.496 86.046 1879 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.51 % Favored : 91.29 % Rotamer: Outliers : 2.05 % Allowed : 19.24 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1481 helix: 1.20 (0.19), residues: 809 sheet: -1.55 (0.71), residues: 54 loop : -2.79 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F1474 HIS 0.004 0.001 HIS F1647 PHE 0.022 0.001 PHE F1499 TYR 0.021 0.001 TYR F1800 ARG 0.008 0.000 ARG F 938 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 1) link_NAG-ASN : angle 2.67354 ( 3) link_BETA1-4 : bond 0.00294 ( 1) link_BETA1-4 : angle 4.69851 ( 3) hydrogen bonds : bond 0.04270 ( 528) hydrogen bonds : angle 3.73036 ( 1545) SS BOND : bond 0.00227 ( 2) SS BOND : angle 0.76809 ( 4) covalent geometry : bond 0.00297 (12832) covalent geometry : angle 0.62545 (17304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: F 441 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: F 658 CYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5944 (p) REVERT: F 774 LYS cc_start: 0.9124 (pttt) cc_final: 0.8852 (pttt) REVERT: F 858 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7743 (ttp80) REVERT: F 878 GLN cc_start: 0.9250 (tm-30) cc_final: 0.8883 (tm-30) REVERT: F 1053 ASP cc_start: 0.8687 (t70) cc_final: 0.8347 (t70) REVERT: F 1220 ASN cc_start: 0.7263 (t0) cc_final: 0.6888 (t0) REVERT: F 1327 MET cc_start: 0.9014 (mpp) cc_final: 0.8674 (mpp) REVERT: F 1400 MET cc_start: 0.2604 (tmm) cc_final: 0.1040 (ptp) REVERT: F 1562 MET cc_start: 0.7654 (tmm) cc_final: 0.7382 (tmm) REVERT: F 1736 GLU cc_start: 0.8970 (tp30) cc_final: 0.8628 (tp30) REVERT: F 1739 GLU cc_start: 0.9251 (tt0) cc_final: 0.8817 (tm-30) REVERT: F 1791 ARG cc_start: 0.8953 (ptm-80) cc_final: 0.8517 (ttm110) REVERT: F 1795 ARG cc_start: 0.8651 (tpp-160) cc_final: 0.8134 (tpp-160) REVERT: F 1796 MET cc_start: 0.8488 (ttt) cc_final: 0.7917 (tpt) outliers start: 27 outliers final: 18 residues processed: 170 average time/residue: 0.2477 time to fit residues: 61.3335 Evaluate side-chains 168 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 441 GLU Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 550 PHE Chi-restraints excluded: chain F residue 658 CYS Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 839 MET Chi-restraints excluded: chain F residue 879 LEU Chi-restraints excluded: chain F residue 1088 HIS Chi-restraints excluded: chain F residue 1092 PHE Chi-restraints excluded: chain F residue 1127 VAL Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1452 MET Chi-restraints excluded: chain F residue 1797 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 80 optimal weight: 0.0970 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 51 optimal weight: 8.9990 chunk 94 optimal weight: 30.0000 chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.081803 restraints weight = 25391.598| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.60 r_work: 0.2894 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12836 Z= 0.137 Angle : 0.634 12.282 17314 Z= 0.315 Chirality : 0.041 0.172 1893 Planarity : 0.004 0.070 2142 Dihedral : 6.398 86.138 1879 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.71 % Favored : 91.09 % Rotamer: Outliers : 1.74 % Allowed : 19.55 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1481 helix: 1.26 (0.19), residues: 809 sheet: -1.48 (0.71), residues: 54 loop : -2.79 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F1474 HIS 0.004 0.001 HIS F1647 PHE 0.008 0.001 PHE F1287 TYR 0.016 0.001 TYR F1330 ARG 0.008 0.000 ARG F 938 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 1) link_NAG-ASN : angle 2.64510 ( 3) link_BETA1-4 : bond 0.00212 ( 1) link_BETA1-4 : angle 4.58635 ( 3) hydrogen bonds : bond 0.04391 ( 528) hydrogen bonds : angle 3.72710 ( 1545) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.77575 ( 4) covalent geometry : bond 0.00311 (12832) covalent geometry : angle 0.63030 (17304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.456 Fit side-chains REVERT: F 441 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: F 658 CYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5978 (p) REVERT: F 774 LYS cc_start: 0.9122 (pttt) cc_final: 0.8882 (pttt) REVERT: F 858 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7738 (ttp80) REVERT: F 878 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8948 (tm-30) REVERT: F 991 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8389 (mm-30) REVERT: F 1053 ASP cc_start: 0.8673 (t70) cc_final: 0.8335 (t70) REVERT: F 1220 ASN cc_start: 0.7270 (t0) cc_final: 0.6889 (t0) REVERT: F 1327 MET cc_start: 0.9017 (mpp) cc_final: 0.8626 (mpp) REVERT: F 1400 MET cc_start: 0.2657 (tmm) cc_final: 0.1047 (ptp) REVERT: F 1562 MET cc_start: 0.7818 (tmm) cc_final: 0.7521 (tmm) REVERT: F 1736 GLU cc_start: 0.8968 (tp30) cc_final: 0.8609 (tp30) REVERT: F 1739 GLU cc_start: 0.9257 (tt0) cc_final: 0.8802 (tm-30) REVERT: F 1795 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8220 (tpp-160) REVERT: F 1796 MET cc_start: 0.8382 (ttt) cc_final: 0.7828 (tpt) outliers start: 23 outliers final: 18 residues processed: 170 average time/residue: 0.2522 time to fit residues: 62.5700 Evaluate side-chains 171 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 441 GLU Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 550 PHE Chi-restraints excluded: chain F residue 658 CYS Chi-restraints excluded: chain F residue 730 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 839 MET Chi-restraints excluded: chain F residue 879 LEU Chi-restraints excluded: chain F residue 1088 HIS Chi-restraints excluded: chain F residue 1092 PHE Chi-restraints excluded: chain F residue 1127 VAL Chi-restraints excluded: chain F residue 1144 THR Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1346 TYR Chi-restraints excluded: chain F residue 1371 VAL Chi-restraints excluded: chain F residue 1452 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 85 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.081447 restraints weight = 25684.092| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.62 r_work: 0.2887 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12836 Z= 0.140 Angle : 0.639 12.607 17314 Z= 0.316 Chirality : 0.041 0.171 1893 Planarity : 0.004 0.076 2142 Dihedral : 6.404 85.773 1879 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.71 % Favored : 91.02 % Rotamer: Outliers : 1.89 % Allowed : 19.77 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.23), residues: 1481 helix: 1.25 (0.19), residues: 810 sheet: -1.44 (0.71), residues: 54 loop : -2.80 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F1474 HIS 0.004 0.001 HIS F1647 PHE 0.021 0.001 PHE F1499 TYR 0.019 0.001 TYR F1800 ARG 0.008 0.000 ARG F 938 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 1) link_NAG-ASN : angle 2.60736 ( 3) link_BETA1-4 : bond 0.00243 ( 1) link_BETA1-4 : angle 4.50989 ( 3) hydrogen bonds : bond 0.04410 ( 528) hydrogen bonds : angle 3.74907 ( 1545) SS BOND : bond 0.00258 ( 2) SS BOND : angle 0.78217 ( 4) covalent geometry : bond 0.00321 (12832) covalent geometry : angle 0.63576 (17304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7479.28 seconds wall clock time: 135 minutes 0.72 seconds (8100.72 seconds total)