Starting phenix.real_space_refine on Thu Mar 5 12:11:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pw5_13675/03_2026/7pw5_13675_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pw5_13675/03_2026/7pw5_13675.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/7pw5_13675/03_2026/7pw5_13675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pw5_13675/03_2026/7pw5_13675.map" model { file = "/net/cci-nas-00/data/ceres_data/7pw5_13675/03_2026/7pw5_13675_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pw5_13675/03_2026/7pw5_13675_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.058 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: 7 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 113 5.16 5 Cl 1 4.86 5 C 13837 2.51 5 N 3811 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21548 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1295, 9176 Classifications: {'peptide': 1295} Incomplete info: {'truncation_to_alanine': 337} Link IDs: {'PTRANS': 35, 'TRANS': 1259} Chain breaks: 25 Unresolved non-hydrogen bonds: 926 Unresolved non-hydrogen angles: 1214 Unresolved non-hydrogen dihedrals: 672 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'UNK:plan-1': 121, 'PHE:plan': 5, 'ASN:plan1': 13, 'ARG:plan': 4, 'ASP:plan': 32, 'GLN:plan1': 9, 'TRP:plan': 2, 'GLU:plan': 44, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 560 Chain: "A" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1423 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain breaks: 6 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'UNK:plan-1': 42, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 8, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 159 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 196 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 16, 'GLU:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2929 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'UNK:plan-1': 16, 'ARG:plan': 3, 'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 7, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5296 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 646} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 7, 'ASP:plan': 13, 'GLU:plan': 15, 'ASN:plan1': 5, 'GLN:plan1': 8, 'PHE:plan': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 249 Chain: "C" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2421 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 292} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'88C': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG C 602 " occ=0.00 Time building chain proxies: 4.87, per 1000 atoms: 0.23 Number of scatterers: 21548 At special positions: 0 Unit cell: (125.978, 160.877, 182.157, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 113 16.00 P 9 15.00 Mg 1 11.99 O 3776 8.00 N 3811 7.00 C 13837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5684 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 12 sheets defined 67.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.776A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.627A pdb=" N UNK A 234 " --> pdb=" O UNK A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 265 removed outlier: 3.938A pdb=" N UNK A 265 " --> pdb=" O UNK A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.912A pdb=" N UNK A 284 " --> pdb=" O UNK A 280 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N UNK A 285 " --> pdb=" O UNK A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.987A pdb=" N UNK A 303 " --> pdb=" O UNK A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.946A pdb=" N ASP A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 removed outlier: 3.557A pdb=" N VAL A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 376 removed outlier: 4.115A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 428 through 444 removed outlier: 4.480A pdb=" N VAL A 432 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 467 removed outlier: 4.014A pdb=" N LEU A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.910A pdb=" N ILE A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.976A pdb=" N VAL A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.783A pdb=" N ARG A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 554 removed outlier: 3.624A pdb=" N VAL A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 583 removed outlier: 4.056A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.752A pdb=" N LYS A 593 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.522A pdb=" N PHE A 597 " --> pdb=" O HIS A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 618 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.778A pdb=" N HIS A 650 " --> pdb=" O MET A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.872A pdb=" N HIS A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 674 removed outlier: 4.018A pdb=" N GLN A 661 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'A' and resid 724 through 745 removed outlier: 3.738A pdb=" N ARG A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 744 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 Processing helix chain 'A' and resid 754 through 768 removed outlier: 3.741A pdb=" N HIS A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 768 " --> pdb=" O LEU A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 removed outlier: 3.652A pdb=" N CYS A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 786 " --> pdb=" O SER A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 806 Processing helix chain 'A' and resid 811 through 823 Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 835 through 851 Processing helix chain 'A' and resid 858 through 871 Processing helix chain 'A' and resid 882 through 890 Processing helix chain 'A' and resid 902 through 907 removed outlier: 4.113A pdb=" N LYS A 907 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 927 Processing helix chain 'A' and resid 935 through 956 removed outlier: 3.592A pdb=" N THR A 939 " --> pdb=" O ARG A 935 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 956 " --> pdb=" O ALA A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 999 removed outlier: 3.916A pdb=" N HIS A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1019 removed outlier: 3.899A pdb=" N THR A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.597A pdb=" N CYS A1023 " --> pdb=" O ASN A1019 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1058 removed outlier: 3.764A pdb=" N THR A1047 " --> pdb=" O GLN A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1083 removed outlier: 3.601A pdb=" N THR A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1097 Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.767A pdb=" N VAL A1110 " --> pdb=" O TRP A1106 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A1115 " --> pdb=" O ALA A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1134 Processing helix chain 'A' and resid 1143 through 1151 Processing helix chain 'A' and resid 1179 through 1197 Processing helix chain 'A' and resid 1199 through 1218 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.605A pdb=" N ILE A1231 " --> pdb=" O ASP A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1250 removed outlier: 3.540A pdb=" N GLU A1247 " --> pdb=" O VAL A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1305 Processing helix chain 'A' and resid 1317 through 1332 removed outlier: 3.883A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A1332 " --> pdb=" O SER A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1341 removed outlier: 3.540A pdb=" N THR A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1340 " --> pdb=" O ARG A1336 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A1341 " --> pdb=" O LEU A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1367 removed outlier: 3.608A pdb=" N SER A1365 " --> pdb=" O GLU A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1374 removed outlier: 3.644A pdb=" N LEU A1374 " --> pdb=" O GLU A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1383 removed outlier: 3.588A pdb=" N ARG A1383 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1407 removed outlier: 3.659A pdb=" N MET A1394 " --> pdb=" O VAL A1390 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A1395 " --> pdb=" O ARG A1391 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A1396 " --> pdb=" O PRO A1392 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A1403 " --> pdb=" O TYR A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1410 No H-bonds generated for 'chain 'A' and resid 1408 through 1410' Processing helix chain 'A' and resid 1417 through 1435 removed outlier: 3.517A pdb=" N ARG A1435 " --> pdb=" O PHE A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1450 Processing helix chain 'A' and resid 1458 through 1467 removed outlier: 3.725A pdb=" N LEU A1462 " --> pdb=" O THR A1458 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A1463 " --> pdb=" O ALA A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1494 Processing helix chain 'A' and resid 1496 through 1512 Processing helix chain 'A' and resid 1520 through 1535 Processing helix chain 'A' and resid 1539 through 1551 removed outlier: 3.634A pdb=" N LEU A1543 " --> pdb=" O ILE A1539 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A1551 " --> pdb=" O TYR A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1570 Processing helix chain 'A' and resid 1588 through 1592 removed outlier: 3.906A pdb=" N ILE A1592 " --> pdb=" O THR A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1612 removed outlier: 4.159A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1637 removed outlier: 4.365A pdb=" N TRP A1619 " --> pdb=" O VAL A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1656 Processing helix chain 'A' and resid 1664 through 1674 removed outlier: 3.579A pdb=" N UNK A1674 " --> pdb=" O UNK A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1717 Processing helix chain 'A' and resid 1728 through 1740 removed outlier: 3.569A pdb=" N ASP A1738 " --> pdb=" O ARG A1734 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A1739 " --> pdb=" O LYS A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1757 Processing helix chain 'A' and resid 1781 through 1799 removed outlier: 3.526A pdb=" N MET A1787 " --> pdb=" O ASP A1783 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A1788 " --> pdb=" O MET A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1811 removed outlier: 3.549A pdb=" N LEU A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1822 through 1829 Processing helix chain 'A' and resid 1835 through 1850 removed outlier: 3.576A pdb=" N GLN A1850 " --> pdb=" O CYS A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1865 removed outlier: 3.605A pdb=" N ALA A1860 " --> pdb=" O ILE A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1938 removed outlier: 4.029A pdb=" N CYS A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A1930 " --> pdb=" O MET A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1958 Processing helix chain 'A' and resid 1963 through 1978 removed outlier: 4.349A pdb=" N LEU A1978 " --> pdb=" O HIS A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 2007 through 2021 Processing helix chain 'A' and resid 2036 through 2044 Processing helix chain 'A' and resid 2046 through 2056 removed outlier: 4.016A pdb=" N LYS A2056 " --> pdb=" O LEU A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2083 removed outlier: 3.794A pdb=" N UNK A2083 " --> pdb=" O UNK A2079 " (cutoff:3.500A) Processing helix chain 'A' and resid 2160 through 2176 removed outlier: 3.535A pdb=" N GLU A2164 " --> pdb=" O LEU A2160 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET A2176 " --> pdb=" O ILE A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2177 through 2178 No H-bonds generated for 'chain 'A' and resid 2177 through 2178' Processing helix chain 'A' and resid 2179 through 2184 removed outlier: 3.819A pdb=" N GLN A2183 " --> pdb=" O ILE A2180 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A2184 " --> pdb=" O ASN A2181 " (cutoff:3.500A) Processing helix chain 'A' and resid 2214 through 2232 removed outlier: 3.753A pdb=" N TYR A2218 " --> pdb=" O LEU A2214 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A2231 " --> pdb=" O ALA A2227 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A2232 " --> pdb=" O LEU A2228 " (cutoff:3.500A) Processing helix chain 'A' and resid 2248 through 2265 removed outlier: 3.545A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Proline residue: A2259 - end of helix Processing helix chain 'A' and resid 2276 through 2289 removed outlier: 3.577A pdb=" N MET A2280 " --> pdb=" O PRO A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2304 Processing helix chain 'A' and resid 2306 through 2332 Processing helix chain 'A' and resid 2361 through 2365 removed outlier: 3.611A pdb=" N SER A2364 " --> pdb=" O LYS A2361 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A2365 " --> pdb=" O GLY A2362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2361 through 2365' Processing helix chain 'A' and resid 2376 through 2382 Processing helix chain 'A' and resid 2390 through 2406 removed outlier: 3.658A pdb=" N LEU A2394 " --> pdb=" O GLY A2390 " (cutoff:3.500A) Processing helix chain 'A' and resid 2406 through 2419 removed outlier: 3.940A pdb=" N LEU A2410 " --> pdb=" O GLY A2406 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3622 Processing helix chain 'A' and resid 3632 through 3644 Processing helix chain 'A' and resid 3646 through 3651 removed outlier: 3.544A pdb=" N LEU A3650 " --> pdb=" O ASN A3646 " (cutoff:3.500A) Processing helix chain 'A' and resid 3654 through 3658 Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.021A pdb=" N MET B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.522A pdb=" N ARG B 43 " --> pdb=" O PRO B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 73 Processing helix chain 'B' and resid 158 through 172 removed outlier: 3.588A pdb=" N ARG B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 204 removed outlier: 4.058A pdb=" N HIS B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 245 removed outlier: 3.975A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.652A pdb=" N THR B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 296 through 315 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 409 through 423 removed outlier: 4.254A pdb=" N HIS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.816A pdb=" N ALA B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 489 through 509 Proline residue: B 505 - end of helix Processing helix chain 'B' and resid 524 through 539 Processing helix chain 'B' and resid 543 through 557 removed outlier: 4.005A pdb=" N TYR B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR B 556 " --> pdb=" O HIS B 552 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 557 " --> pdb=" O GLU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 631 Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 773 through 777 Processing helix chain 'B' and resid 838 through 840 No H-bonds generated for 'chain 'B' and resid 838 through 840' Processing helix chain 'B' and resid 878 through 884 removed outlier: 4.534A pdb=" N ALA B 882 " --> pdb=" O SER B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 977 No H-bonds generated for 'chain 'B' and resid 975 through 977' Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 216 through 226 Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.841A pdb=" N TYR C 236 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.734A pdb=" N GLU C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.958A pdb=" N ASN C 284 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 315 removed outlier: 3.964A pdb=" N GLU C 301 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 380 through 395 removed outlier: 3.513A pdb=" N GLN C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 removed outlier: 4.003A pdb=" N ASN C 412 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 422 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 465 through 479 Processing helix chain 'C' and resid 491 through 508 Processing helix chain 'C' and resid 510 through 518 removed outlier: 3.672A pdb=" N LEU C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2123 through 2124 removed outlier: 3.832A pdb=" N SER A2123 " --> pdb=" O LEU A2143 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A2143 " --> pdb=" O SER A2123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 2129 through 2130 removed outlier: 3.849A pdb=" N LYS A2138 " --> pdb=" O PHE A2154 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A2152 " --> pdb=" O LEU A2140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2212 through 2213 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.046A pdb=" N CYS B 48 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 151 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 50 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU B 153 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE B 52 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL B 49 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU B 211 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY B 51 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL B 213 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE B 53 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N TYR B 337 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 267 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL B 339 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE B 269 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 606 through 610 Processing sheet with id=AA6, first strand: chain 'B' and resid 646 through 648 removed outlier: 3.996A pdb=" N ASP B 646 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B 768 " --> pdb=" O ILE B 648 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 951 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU B 907 " --> pdb=" O GLU B 852 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU B 852 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 13.348A pdb=" N VAL B 847 " --> pdb=" O GLY B 863 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N GLY B 863 " --> pdb=" O VAL B 847 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B 849 " --> pdb=" O CYS B 861 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS B 866 " --> pdb=" O SER B 862 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 796 through 801 removed outlier: 6.452A pdb=" N GLU B 852 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU B 907 " --> pdb=" O GLU B 852 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 661 through 662 removed outlier: 6.907A pdb=" N ALA B 661 " --> pdb=" O TYR B 746 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 887 through 888 Processing sheet with id=AB1, first strand: chain 'B' and resid 944 through 946 removed outlier: 4.588A pdb=" N ILE B 921 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 960 through 962 removed outlier: 4.698A pdb=" N TYR B 960 " --> pdb=" O CYS B 967 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 184 removed outlier: 6.634A pdb=" N ILE C 256 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU C 205 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU C 268 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL C 206 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE C 319 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY C 208 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL C 321 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU C 210 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 318 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU C 370 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL C 320 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN C 372 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN C 322 " --> pdb=" O ASN C 372 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA C 374 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N PHE C 429 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE C 369 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL C 431 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN C 371 " --> pdb=" O VAL C 431 " (cutoff:3.500A) 1242 hydrogen bonds defined for protein. 3594 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: 4.01 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3430 1.31 - 1.44: 5710 1.44 - 1.57: 12649 1.57 - 1.69: 11 1.69 - 1.82: 171 Bond restraints: 21971 Sorted by residual: bond pdb=" C28 88C A3702 " pdb=" N30 88C A3702 " ideal model delta sigma weight residual 1.352 1.453 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" CA PRO B 947 " pdb=" C PRO B 947 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.23e+01 bond pdb=" C13 88C A3702 " pdb=" N12 88C A3702 " ideal model delta sigma weight residual 1.364 1.456 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C22 88C A3702 " pdb=" C23 88C A3702 " ideal model delta sigma weight residual 1.476 1.386 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C17 88C A3702 " pdb=" C18 88C A3702 " ideal model delta sigma weight residual 1.480 1.391 0.089 2.00e-02 2.50e+03 1.98e+01 ... (remaining 21966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 29668 3.33 - 6.66: 294 6.66 - 9.99: 18 9.99 - 13.32: 0 13.32 - 16.64: 1 Bond angle restraints: 29981 Sorted by residual: angle pdb=" N GLU A 746 " pdb=" CA GLU A 746 " pdb=" C GLU A 746 " ideal model delta sigma weight residual 113.30 104.51 8.79 1.34e+00 5.57e-01 4.30e+01 angle pdb=" OE1 GLN B 991 " pdb=" CD GLN B 991 " pdb=" NE2 GLN B 991 " ideal model delta sigma weight residual 122.60 116.74 5.86 1.00e+00 1.00e+00 3.44e+01 angle pdb=" CA PRO A1392 " pdb=" N PRO A1392 " pdb=" CD PRO A1392 " ideal model delta sigma weight residual 112.00 103.82 8.18 1.40e+00 5.10e-01 3.41e+01 angle pdb=" O07 88C A3702 " pdb=" S06 88C A3702 " pdb=" O08 88C A3702 " ideal model delta sigma weight residual 117.67 101.03 16.64 3.00e+00 1.11e-01 3.08e+01 angle pdb=" N VAL A 393 " pdb=" CA VAL A 393 " pdb=" C VAL A 393 " ideal model delta sigma weight residual 113.20 108.01 5.19 9.60e-01 1.09e+00 2.92e+01 ... (remaining 29976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 12899 34.64 - 69.28: 224 69.28 - 103.91: 18 103.91 - 138.55: 2 138.55 - 173.19: 3 Dihedral angle restraints: 13146 sinusoidal: 4477 harmonic: 8669 Sorted by residual: dihedral pdb=" CA ARG B 803 " pdb=" C ARG B 803 " pdb=" N THR B 804 " pdb=" CA THR B 804 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" O12 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O13 IHP A3701 " ideal model delta sinusoidal sigma weight residual 64.08 -109.11 173.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 60.90 -129.71 -169.39 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 3611 0.990 - 1.980: 0 1.980 - 2.969: 0 2.969 - 3.959: 0 3.959 - 4.949: 3 Chirality restraints: 3614 Sorted by residual: chirality pdb=" C2 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " both_signs ideal model delta sigma weight residual False -2.52 2.43 -4.95 2.00e-01 2.50e+01 6.12e+02 chirality pdb=" C4 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" C5 IHP A3701 " pdb=" O14 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.48 -2.38 4.86 2.00e-01 2.50e+01 5.90e+02 chirality pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C6 IHP A3701 " pdb=" O11 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.32 -2.50 4.81 2.00e-01 2.50e+01 5.79e+02 ... (remaining 3611 not shown) Planarity restraints: 3761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 777 " 0.103 2.00e-02 2.50e+03 6.00e-02 7.20e+01 pdb=" CG TYR B 777 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 777 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR B 777 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR B 777 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR B 777 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR B 777 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 777 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 634 " -0.078 2.00e-02 2.50e+03 4.40e-02 3.88e+01 pdb=" CG TYR B 634 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 634 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 634 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 TYR B 634 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR B 634 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 634 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 634 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 552 " 0.027 2.00e-02 2.50e+03 5.42e-02 2.94e+01 pdb=" C HIS B 552 " -0.094 2.00e-02 2.50e+03 pdb=" O HIS B 552 " 0.035 2.00e-02 2.50e+03 pdb=" N GLU B 553 " 0.031 2.00e-02 2.50e+03 ... (remaining 3758 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 97 2.60 - 3.18: 17888 3.18 - 3.75: 32355 3.75 - 4.33: 41385 4.33 - 4.90: 71683 Nonbonded interactions: 163408 Sorted by model distance: nonbonded pdb=" OG1 THR C 253 " pdb="MG MG C 602 " model vdw 2.030 2.170 nonbonded pdb=" OG SER C 218 " pdb="MG MG C 602 " model vdw 2.064 2.170 nonbonded pdb=" O ASN B 561 " pdb=" ND2 ASN B 561 " model vdw 2.074 3.120 nonbonded pdb=" OE1 GLN A1126 " pdb=" OH TYR A1194 " model vdw 2.100 3.040 nonbonded pdb=" OH TYR A 669 " pdb=" OE1 GLU A 737 " model vdw 2.208 3.040 ... (remaining 163403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.530 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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: 0.020 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 21972 Z= 0.312 Angle : 0.831 16.645 29981 Z= 0.504 Chirality : 0.148 4.949 3614 Planarity : 0.007 0.160 3761 Dihedral : 13.917 173.191 7462 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.03 % Favored : 96.86 % Rotamer: Outliers : 0.20 % Allowed : 0.66 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.17), residues: 2677 helix: 2.32 (0.14), residues: 1497 sheet: -0.35 (0.36), residues: 198 loop : -1.20 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 955 TYR 0.103 0.003 TYR B 777 PHE 0.038 0.002 PHE B 911 TRP 0.037 0.002 TRP B 766 HIS 0.017 0.001 HIS B 752 Details of bonding type rmsd covalent geometry : bond 0.00548 (21971) covalent geometry : angle 0.83062 (29981) hydrogen bonds : bond 0.14313 ( 1236) hydrogen bonds : angle 4.39395 ( 3594) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 326 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1950 MET cc_start: 0.6328 (tmm) cc_final: 0.6121 (ppp) REVERT: B 804 THR cc_start: 0.1647 (OUTLIER) cc_final: 0.1156 (m) REVERT: B 860 MET cc_start: 0.2233 (mmt) cc_final: 0.1123 (mmt) outliers start: 4 outliers final: 1 residues processed: 330 average time/residue: 0.1446 time to fit residues: 75.8347 Evaluate side-chains 168 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 955 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 GLN A1344 GLN A1550 GLN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS C 484 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.096125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.067426 restraints weight = 68889.264| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.80 r_work: 0.3230 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 21972 Z= 0.162 Angle : 0.630 12.246 29981 Z= 0.302 Chirality : 0.040 0.270 3614 Planarity : 0.005 0.071 3761 Dihedral : 8.343 117.577 3216 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 1.41 % Allowed : 9.32 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2677 helix: 2.06 (0.14), residues: 1539 sheet: -0.34 (0.36), residues: 203 loop : -1.07 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 569 TYR 0.021 0.002 TYR A1230 PHE 0.038 0.002 PHE A1599 TRP 0.024 0.002 TRP B 952 HIS 0.012 0.001 HIS B 575 Details of bonding type rmsd covalent geometry : bond 0.00365 (21971) covalent geometry : angle 0.62993 (29981) hydrogen bonds : bond 0.04004 ( 1236) hydrogen bonds : angle 3.60482 ( 3594) Misc. bond : bond 0.00160 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 585 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7254 (mp) REVERT: A 722 ASN cc_start: 0.8583 (m-40) cc_final: 0.8333 (t0) REVERT: A 1185 TYR cc_start: 0.8238 (t80) cc_final: 0.7985 (t80) REVERT: A 3631 MET cc_start: 0.8183 (mtp) cc_final: 0.7950 (mtp) REVERT: B 196 GLN cc_start: 0.7839 (tt0) cc_final: 0.7507 (tt0) REVERT: B 750 MET cc_start: 0.4868 (ttt) cc_final: 0.4101 (tpt) REVERT: B 868 MET cc_start: 0.6684 (mtp) cc_final: 0.6025 (mtp) REVERT: C 188 MET cc_start: 0.8765 (mmp) cc_final: 0.8514 (mmp) REVERT: C 383 LYS cc_start: 0.8266 (tptt) cc_final: 0.8058 (mmmt) outliers start: 28 outliers final: 15 residues processed: 184 average time/residue: 0.1283 time to fit residues: 39.7343 Evaluate side-chains 156 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1550 GLN Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 3620 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 223 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 2 optimal weight: 50.0000 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 209 optimal weight: 0.9990 chunk 217 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 231 optimal weight: 0.0030 chunk 108 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 HIS A1550 GLN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN C 213 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.096421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.067630 restraints weight = 68872.300| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.86 r_work: 0.3237 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21972 Z= 0.100 Angle : 0.511 11.697 29981 Z= 0.245 Chirality : 0.037 0.323 3614 Planarity : 0.004 0.061 3761 Dihedral : 8.230 125.684 3211 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.95 % Rotamer: Outliers : 1.41 % Allowed : 11.24 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.17), residues: 2677 helix: 2.31 (0.14), residues: 1532 sheet: -0.16 (0.36), residues: 204 loop : -0.95 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 955 TYR 0.016 0.001 TYR A 998 PHE 0.021 0.001 PHE A2392 TRP 0.020 0.001 TRP B 798 HIS 0.005 0.001 HIS A1606 Details of bonding type rmsd covalent geometry : bond 0.00223 (21971) covalent geometry : angle 0.51079 (29981) hydrogen bonds : bond 0.03351 ( 1236) hydrogen bonds : angle 3.31531 ( 3594) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 533 LEU cc_start: 0.9119 (mt) cc_final: 0.8898 (mt) REVERT: A 722 ASN cc_start: 0.8636 (m-40) cc_final: 0.8353 (t0) REVERT: A 1185 TYR cc_start: 0.8186 (t80) cc_final: 0.7931 (t80) REVERT: A 1270 MET cc_start: 0.7779 (tpp) cc_final: 0.7282 (mmt) REVERT: A 1784 MET cc_start: 0.7146 (tpt) cc_final: 0.6746 (ttt) REVERT: A 2375 MET cc_start: 0.7941 (tpt) cc_final: 0.7707 (tpt) REVERT: B 868 MET cc_start: 0.7304 (mtp) cc_final: 0.6586 (mtp) REVERT: B 887 MET cc_start: 0.0382 (mtt) cc_final: 0.0023 (ptt) REVERT: B 977 MET cc_start: 0.9546 (mmp) cc_final: 0.9002 (ppp) REVERT: C 383 LYS cc_start: 0.8233 (tptt) cc_final: 0.7979 (mmmt) REVERT: C 387 MET cc_start: 0.8257 (mtp) cc_final: 0.7917 (mmm) outliers start: 28 outliers final: 16 residues processed: 166 average time/residue: 0.1270 time to fit residues: 35.9252 Evaluate side-chains 150 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 428 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 138 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN A 510 GLN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1258 ASN A1550 GLN B 159 ASN B 498 ASN B 617 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.089424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.060333 restraints weight = 71912.417| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.71 r_work: 0.3066 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 21972 Z= 0.241 Angle : 0.695 10.624 29981 Z= 0.345 Chirality : 0.043 0.263 3614 Planarity : 0.005 0.090 3761 Dihedral : 8.476 123.543 3211 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 2.67 % Allowed : 11.95 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.17), residues: 2677 helix: 1.68 (0.13), residues: 1537 sheet: -0.21 (0.37), residues: 199 loop : -1.06 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1443 TYR 0.024 0.002 TYR A1323 PHE 0.028 0.003 PHE B 580 TRP 0.021 0.002 TRP B 798 HIS 0.015 0.002 HIS B 575 Details of bonding type rmsd covalent geometry : bond 0.00570 (21971) covalent geometry : angle 0.69490 (29981) hydrogen bonds : bond 0.05380 ( 1236) hydrogen bonds : angle 3.91176 ( 3594) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 0.737 Fit side-chains REVERT: A 506 LEU cc_start: 0.9577 (mt) cc_final: 0.9313 (tt) REVERT: B 750 MET cc_start: 0.4922 (ttt) cc_final: 0.4096 (tpt) REVERT: B 868 MET cc_start: 0.6866 (mtp) cc_final: 0.5738 (mtt) REVERT: B 887 MET cc_start: 0.0290 (mtt) cc_final: 0.0065 (ptt) REVERT: C 247 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7911 (mt-10) REVERT: C 412 ASN cc_start: 0.9199 (t0) cc_final: 0.8993 (t0) outliers start: 53 outliers final: 31 residues processed: 160 average time/residue: 0.1347 time to fit residues: 35.9246 Evaluate side-chains 143 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1550 GLN Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 387 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 209 optimal weight: 0.0670 chunk 237 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 199 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN A1395 GLN A1550 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.092152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.063025 restraints weight = 70043.697| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.87 r_work: 0.3127 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21972 Z= 0.102 Angle : 0.516 10.909 29981 Z= 0.249 Chirality : 0.037 0.291 3614 Planarity : 0.004 0.056 3761 Dihedral : 8.254 123.725 3211 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.24 % Favored : 97.72 % Rotamer: Outliers : 1.97 % Allowed : 13.26 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.17), residues: 2677 helix: 2.22 (0.14), residues: 1539 sheet: -0.17 (0.35), residues: 210 loop : -0.95 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1013 TYR 0.017 0.001 TYR A 998 PHE 0.023 0.001 PHE A2392 TRP 0.019 0.001 TRP B 798 HIS 0.004 0.001 HIS A1551 Details of bonding type rmsd covalent geometry : bond 0.00223 (21971) covalent geometry : angle 0.51605 (29981) hydrogen bonds : bond 0.03534 ( 1236) hydrogen bonds : angle 3.32518 ( 3594) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.702 Fit side-chains REVERT: A 506 LEU cc_start: 0.9543 (mt) cc_final: 0.9265 (tt) REVERT: A 1270 MET cc_start: 0.7857 (tpp) cc_final: 0.7647 (mmt) REVERT: A 2375 MET cc_start: 0.8416 (mmm) cc_final: 0.8129 (mmm) REVERT: B 750 MET cc_start: 0.5449 (ttt) cc_final: 0.4622 (tpt) REVERT: B 868 MET cc_start: 0.6489 (mtp) cc_final: 0.5923 (mtp) REVERT: B 887 MET cc_start: 0.0396 (mtt) cc_final: -0.0026 (ptp) REVERT: B 977 MET cc_start: 0.9561 (mmp) cc_final: 0.9069 (ppp) REVERT: C 247 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7810 (mt-10) REVERT: C 327 ASP cc_start: 0.8486 (t0) cc_final: 0.8250 (t70) REVERT: C 386 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8218 (mp10) REVERT: C 412 ASN cc_start: 0.9168 (t0) cc_final: 0.8949 (t0) outliers start: 39 outliers final: 21 residues processed: 155 average time/residue: 0.1168 time to fit residues: 31.1785 Evaluate side-chains 132 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1058 MET Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1395 GLN Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1550 GLN Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 387 MET Chi-restraints excluded: chain C residue 428 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 144 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 142 optimal weight: 0.3980 chunk 229 optimal weight: 7.9990 chunk 263 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN B 196 GLN ** C 297 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 = 0.3849 r_free = 0.3849 target = 0.090160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.060895 restraints weight = 71740.341| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.86 r_work: 0.3075 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21972 Z= 0.169 Angle : 0.565 10.864 29981 Z= 0.274 Chirality : 0.039 0.280 3614 Planarity : 0.004 0.063 3761 Dihedral : 8.194 123.406 3211 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 2.67 % Allowed : 12.85 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.17), residues: 2677 helix: 2.21 (0.14), residues: 1533 sheet: -0.16 (0.36), residues: 208 loop : -0.93 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2405 TYR 0.017 0.001 TYR B 851 PHE 0.018 0.002 PHE A1599 TRP 0.017 0.001 TRP B 798 HIS 0.004 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00401 (21971) covalent geometry : angle 0.56505 (29981) hydrogen bonds : bond 0.04029 ( 1236) hydrogen bonds : angle 3.46816 ( 3594) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 0.974 Fit side-chains REVERT: A 506 LEU cc_start: 0.9555 (mt) cc_final: 0.9295 (tt) REVERT: A 585 LEU cc_start: 0.8694 (mm) cc_final: 0.8479 (mp) REVERT: A 1003 ASN cc_start: 0.7973 (m-40) cc_final: 0.7547 (t0) REVERT: A 1395 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7873 (mp10) REVERT: B 219 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7200 (p90) REVERT: B 750 MET cc_start: 0.5326 (ttt) cc_final: 0.4470 (tpt) REVERT: B 868 MET cc_start: 0.6492 (mtp) cc_final: 0.5893 (mtp) REVERT: B 887 MET cc_start: 0.0076 (mtt) cc_final: -0.0201 (ptt) REVERT: C 247 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7838 (mt-10) REVERT: C 327 ASP cc_start: 0.8509 (t0) cc_final: 0.8254 (t70) REVERT: C 328 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8575 (tt) REVERT: C 394 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8441 (mp) REVERT: C 412 ASN cc_start: 0.9238 (t0) cc_final: 0.8965 (t0) outliers start: 53 outliers final: 33 residues processed: 155 average time/residue: 0.1218 time to fit residues: 32.4338 Evaluate side-chains 144 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1324 LEU Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1394 MET Chi-restraints excluded: chain A residue 1395 GLN Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2350 VAL Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 502 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 247 optimal weight: 50.0000 chunk 182 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 275 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN A 645 ASN A 875 HIS A1550 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.090686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061386 restraints weight = 71441.643| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.84 r_work: 0.3091 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21972 Z= 0.136 Angle : 0.536 11.250 29981 Z= 0.257 Chirality : 0.038 0.287 3614 Planarity : 0.004 0.055 3761 Dihedral : 8.052 122.419 3211 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 2.42 % Allowed : 13.41 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.17), residues: 2677 helix: 2.30 (0.14), residues: 1538 sheet: -0.15 (0.36), residues: 207 loop : -0.84 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2405 TYR 0.019 0.001 TYR A1125 PHE 0.017 0.001 PHE A1599 TRP 0.018 0.001 TRP B 798 HIS 0.004 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00320 (21971) covalent geometry : angle 0.53555 (29981) hydrogen bonds : bond 0.03557 ( 1236) hydrogen bonds : angle 3.33846 ( 3594) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 116 time to evaluate : 0.697 Fit side-chains REVERT: A 506 LEU cc_start: 0.9553 (mt) cc_final: 0.9294 (tt) REVERT: A 585 LEU cc_start: 0.8741 (mm) cc_final: 0.8495 (mp) REVERT: A 1003 ASN cc_start: 0.7990 (m-40) cc_final: 0.7618 (t0) REVERT: A 1395 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: A 1440 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7399 (tt) REVERT: B 750 MET cc_start: 0.5321 (ttt) cc_final: 0.4624 (tpt) REVERT: B 868 MET cc_start: 0.6229 (mtp) cc_final: 0.5644 (mtp) REVERT: B 887 MET cc_start: -0.0034 (mtt) cc_final: -0.0299 (ptp) REVERT: B 977 MET cc_start: 0.9564 (mmp) cc_final: 0.9081 (ppp) REVERT: C 172 LEU cc_start: 0.8659 (tp) cc_final: 0.8342 (pt) REVERT: C 394 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8496 (mt) REVERT: C 412 ASN cc_start: 0.9254 (t0) cc_final: 0.8964 (t0) outliers start: 48 outliers final: 30 residues processed: 153 average time/residue: 0.1229 time to fit residues: 32.0072 Evaluate side-chains 142 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1058 MET Chi-restraints excluded: chain A residue 1112 GLN Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1395 GLN Chi-restraints excluded: chain A residue 1440 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 502 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 231 optimal weight: 50.0000 chunk 185 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 69 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 252 optimal weight: 50.0000 chunk 286 optimal weight: 7.9990 chunk 168 optimal weight: 0.0070 chunk 181 optimal weight: 1.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.091851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.062569 restraints weight = 70542.184| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.86 r_work: 0.3123 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21972 Z= 0.094 Angle : 0.512 18.237 29981 Z= 0.242 Chirality : 0.037 0.292 3614 Planarity : 0.004 0.053 3761 Dihedral : 7.908 121.186 3211 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 2.02 % Allowed : 13.96 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.17), residues: 2677 helix: 2.48 (0.14), residues: 1531 sheet: 0.04 (0.36), residues: 203 loop : -0.77 (0.22), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2405 TYR 0.018 0.001 TYR A 998 PHE 0.018 0.001 PHE C 325 TRP 0.018 0.001 TRP B 798 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00213 (21971) covalent geometry : angle 0.51182 (29981) hydrogen bonds : bond 0.03053 ( 1236) hydrogen bonds : angle 3.19940 ( 3594) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 506 LEU cc_start: 0.9544 (mt) cc_final: 0.9281 (tt) REVERT: A 585 LEU cc_start: 0.8727 (mm) cc_final: 0.8455 (mp) REVERT: A 1003 ASN cc_start: 0.7957 (m-40) cc_final: 0.7617 (t0) REVERT: A 1395 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: A 1440 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7380 (tt) REVERT: A 2375 MET cc_start: 0.8136 (mmm) cc_final: 0.7819 (mmm) REVERT: B 750 MET cc_start: 0.5450 (ttt) cc_final: 0.4787 (tpt) REVERT: B 868 MET cc_start: 0.6275 (mtp) cc_final: 0.5610 (mtp) REVERT: B 887 MET cc_start: -0.0121 (mtt) cc_final: -0.0350 (ptp) REVERT: B 977 MET cc_start: 0.9580 (mmp) cc_final: 0.9121 (ppp) REVERT: C 172 LEU cc_start: 0.8645 (tp) cc_final: 0.8264 (pt) REVERT: C 412 ASN cc_start: 0.9249 (t0) cc_final: 0.8944 (t0) outliers start: 40 outliers final: 28 residues processed: 151 average time/residue: 0.1216 time to fit residues: 31.9926 Evaluate side-chains 145 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1395 GLN Chi-restraints excluded: chain A residue 1440 LEU Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 1741 PHE Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 3620 LEU Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 502 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 156 optimal weight: 5.9990 chunk 246 optimal weight: 20.0000 chunk 4 optimal weight: 50.0000 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN ** C 297 HIS ** 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 = 0.3853 r_free = 0.3853 target = 0.090238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.060881 restraints weight = 71256.319| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.86 r_work: 0.3082 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21972 Z= 0.145 Angle : 0.550 14.265 29981 Z= 0.263 Chirality : 0.038 0.281 3614 Planarity : 0.004 0.060 3761 Dihedral : 7.902 120.335 3211 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 1.92 % Allowed : 14.52 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.17), residues: 2677 helix: 2.42 (0.14), residues: 1534 sheet: -0.02 (0.36), residues: 203 loop : -0.77 (0.22), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2405 TYR 0.016 0.001 TYR A1125 PHE 0.022 0.001 PHE C 325 TRP 0.016 0.001 TRP B 798 HIS 0.005 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00344 (21971) covalent geometry : angle 0.55031 (29981) hydrogen bonds : bond 0.03683 ( 1236) hydrogen bonds : angle 3.32877 ( 3594) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.866 Fit side-chains REVERT: A 506 LEU cc_start: 0.9558 (mt) cc_final: 0.9312 (tt) REVERT: A 585 LEU cc_start: 0.8833 (mm) cc_final: 0.8560 (mp) REVERT: A 1003 ASN cc_start: 0.7934 (m-40) cc_final: 0.7685 (t0) REVERT: A 1440 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7392 (tt) REVERT: B 750 MET cc_start: 0.5703 (ttt) cc_final: 0.5109 (tpt) REVERT: B 868 MET cc_start: 0.6397 (mtp) cc_final: 0.5760 (mtp) REVERT: B 887 MET cc_start: -0.0188 (mtt) cc_final: -0.0657 (ptp) REVERT: B 977 MET cc_start: 0.9571 (mmp) cc_final: 0.9053 (tpp) REVERT: C 172 LEU cc_start: 0.8671 (tp) cc_final: 0.8266 (pt) REVERT: C 412 ASN cc_start: 0.9282 (t0) cc_final: 0.8980 (t0) outliers start: 38 outliers final: 30 residues processed: 140 average time/residue: 0.1255 time to fit residues: 30.3476 Evaluate side-chains 139 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1440 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 2400 LEU Chi-restraints excluded: chain A residue 3620 LEU Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 502 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.089774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.060480 restraints weight = 71970.242| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.82 r_work: 0.3068 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21972 Z= 0.162 Angle : 0.579 18.274 29981 Z= 0.276 Chirality : 0.039 0.281 3614 Planarity : 0.004 0.064 3761 Dihedral : 7.910 119.810 3211 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 1.92 % Allowed : 14.52 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.17), residues: 2677 helix: 2.34 (0.14), residues: 1532 sheet: -0.10 (0.36), residues: 203 loop : -0.82 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2405 TYR 0.022 0.001 TYR A1125 PHE 0.029 0.001 PHE C 325 TRP 0.022 0.001 TRP B 798 HIS 0.005 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00387 (21971) covalent geometry : angle 0.57889 (29981) hydrogen bonds : bond 0.03819 ( 1236) hydrogen bonds : angle 3.40397 ( 3594) Misc. bond : bond 0.00040 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.745 Fit side-chains REVERT: A 368 MET cc_start: 0.9588 (mtm) cc_final: 0.9172 (mpp) REVERT: A 506 LEU cc_start: 0.9565 (mt) cc_final: 0.9304 (tt) REVERT: A 585 LEU cc_start: 0.8925 (mm) cc_final: 0.8663 (mp) REVERT: A 1440 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7384 (tt) REVERT: B 219 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7410 (p90) REVERT: B 750 MET cc_start: 0.5589 (ttt) cc_final: 0.4991 (tpt) REVERT: B 868 MET cc_start: 0.6162 (mtp) cc_final: 0.5409 (mtp) REVERT: B 887 MET cc_start: -0.0148 (mtt) cc_final: -0.0744 (ptp) REVERT: B 977 MET cc_start: 0.9568 (mmp) cc_final: 0.9048 (tpp) REVERT: C 172 LEU cc_start: 0.8646 (tp) cc_final: 0.8232 (pt) REVERT: C 386 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8508 (mp10) REVERT: C 412 ASN cc_start: 0.9317 (t0) cc_final: 0.9016 (t0) outliers start: 38 outliers final: 31 residues processed: 137 average time/residue: 0.1268 time to fit residues: 29.9750 Evaluate side-chains 137 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1058 MET Chi-restraints excluded: chain A residue 1258 ASN Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1440 LEU Chi-restraints excluded: chain A residue 1590 VAL Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2246 VAL Chi-restraints excluded: chain A residue 2303 SER Chi-restraints excluded: chain A residue 2376 THR Chi-restraints excluded: chain A residue 2400 LEU Chi-restraints excluded: chain A residue 3620 LEU Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 502 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 99 optimal weight: 1.9990 chunk 257 optimal weight: 20.0000 chunk 226 optimal weight: 40.0000 chunk 207 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 119 optimal weight: 0.0670 chunk 132 optimal weight: 20.0000 chunk 74 optimal weight: 0.1980 chunk 112 optimal weight: 0.8980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN A 977 GLN ** C 297 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 = 0.3876 r_free = 0.3876 target = 0.091678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062400 restraints weight = 70363.082| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.88 r_work: 0.3119 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21972 Z= 0.097 Angle : 0.524 15.409 29981 Z= 0.249 Chirality : 0.037 0.299 3614 Planarity : 0.004 0.062 3761 Dihedral : 7.690 118.411 3211 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 1.51 % Allowed : 14.87 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.17), residues: 2677 helix: 2.50 (0.14), residues: 1534 sheet: 0.06 (0.36), residues: 203 loop : -0.72 (0.22), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2405 TYR 0.022 0.001 TYR A1125 PHE 0.018 0.001 PHE C 325 TRP 0.020 0.001 TRP B 798 HIS 0.004 0.001 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00221 (21971) covalent geometry : angle 0.52350 (29981) hydrogen bonds : bond 0.03051 ( 1236) hydrogen bonds : angle 3.18414 ( 3594) Misc. bond : bond 0.00023 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6335.99 seconds wall clock time: 108 minutes 31.69 seconds (6511.69 seconds total)