Starting phenix.real_space_refine on Thu Mar 5 05:50:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pw4_13674/03_2026/7pw4_13674.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pw4_13674/03_2026/7pw4_13674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pw4_13674/03_2026/7pw4_13674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pw4_13674/03_2026/7pw4_13674.map" model { file = "/net/cci-nas-00/data/ceres_data/7pw4_13674/03_2026/7pw4_13674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pw4_13674/03_2026/7pw4_13674.cif" } resolution = 3.27 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= 0.005 sd= 0.076 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 94 5.16 5 Cl 1 4.86 5 C 12188 2.51 5 N 3359 2.21 5 O 3313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 18965 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1295, 9173 Classifications: {'peptide': 1295} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 334} Link IDs: {'PTRANS': 35, 'TRANS': 1259} Chain breaks: 25 Unresolved non-hydrogen bonds: 929 Unresolved non-hydrogen angles: 1220 Unresolved non-hydrogen dihedrals: 672 Unresolved non-hydrogen chiralities: 38 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: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1421 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 98} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain breaks: 6 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 19 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: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2718 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 19, 'TRANS': 356} Chain breaks: 8 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: 4.73, per 1000 atoms: 0.25 Number of scatterers: 18965 At special positions: 0 Unit cell: (120.87, 127.68, 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 94 16.00 P 9 15.00 Mg 1 11.99 O 3313 8.00 N 3359 7.00 C 12188 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: 1.52 Conformation dependent library (CDL) restraints added in 916.8 milliseconds 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5066 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 5 sheets defined 74.8% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 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 743 removed outlier: 3.764A pdb=" N ARG A 743 " --> pdb=" O ALA A 739 " (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 558 removed outlier: 4.005A pdb=" N TYR B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) 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 '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) 1179 hydrogen bonds defined for protein. 3429 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: 3.79 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2960 1.30 - 1.43: 4915 1.43 - 1.56: 11281 1.56 - 1.69: 12 1.69 - 1.82: 143 Bond restraints: 19311 Sorted by residual: bond pdb=" CA LEU A 741 " pdb=" C LEU A 741 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.37e-02 5.33e+03 3.39e+01 bond pdb=" C LYS A 744 " pdb=" O LYS A 744 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.17e-02 7.31e+03 2.75e+01 bond pdb=" C LEU A 741 " pdb=" O LEU A 741 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.32e-02 5.74e+03 2.66e+01 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=" C ARG A 743 " pdb=" O ARG A 743 " ideal model delta sigma weight residual 1.235 1.171 0.065 1.34e-02 5.57e+03 2.32e+01 ... (remaining 19306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 26235 3.33 - 6.66: 118 6.66 - 9.99: 13 9.99 - 13.32: 0 13.32 - 16.64: 1 Bond angle restraints: 26367 Sorted by residual: 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 angle pdb=" N THR C 326 " pdb=" CA THR C 326 " pdb=" C THR C 326 " ideal model delta sigma weight residual 111.02 117.32 -6.30 1.25e+00 6.40e-01 2.54e+01 angle pdb=" N GLN C 213 " pdb=" CA GLN C 213 " pdb=" C GLN C 213 " ideal model delta sigma weight residual 111.03 115.78 -4.75 1.11e+00 8.12e-01 1.83e+01 ... (remaining 26362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 11272 34.64 - 69.28: 211 69.28 - 103.91: 18 103.91 - 138.55: 2 138.55 - 173.19: 3 Dihedral angle restraints: 11506 sinusoidal: 3792 harmonic: 7714 Sorted by residual: 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 dihedral pdb=" C6 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 61.05 -82.07 143.12 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 11503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 3232 0.990 - 1.980: 0 1.980 - 2.969: 0 2.969 - 3.959: 0 3.959 - 4.949: 3 Chirality restraints: 3235 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 3232 not shown) Planarity restraints: 3282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1391 " 0.092 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO A1392 " -0.231 5.00e-02 4.00e+02 pdb=" CA PRO A1392 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO A1392 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 740 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C VAL A 740 " -0.062 2.00e-02 2.50e+03 pdb=" O VAL A 740 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU A 741 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 395 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 396 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " 0.027 5.00e-02 4.00e+02 ... (remaining 3279 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 79 2.60 - 3.18: 15933 3.18 - 3.75: 28608 3.75 - 4.33: 36032 4.33 - 4.90: 62972 Nonbonded interactions: 143624 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=" 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 nonbonded pdb=" OH TYR A2193 " pdb=" O ILE A2353 " model vdw 2.236 3.040 ... (remaining 143619 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: 5.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.210 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 19312 Z= 0.193 Angle : 0.622 16.645 26367 Z= 0.335 Chirality : 0.153 4.949 3235 Planarity : 0.004 0.134 3282 Dihedral : 14.412 173.191 6440 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.69 (0.19), residues: 2355 helix: 2.45 (0.14), residues: 1472 sheet: -0.28 (0.46), residues: 129 loop : -1.43 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 316 TYR 0.016 0.001 TYR A 998 PHE 0.025 0.001 PHE C 325 TRP 0.011 0.001 TRP A2221 HIS 0.003 0.001 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00347 (19311) covalent geometry : angle 0.62210 (26367) hydrogen bonds : bond 0.14212 ( 1179) hydrogen bonds : angle 4.08356 ( 3429) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 1950 MET cc_start: 0.7108 (tmm) cc_final: 0.6423 (tmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1219 time to fit residues: 36.7839 Evaluate side-chains 141 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS A1344 GLN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3691 r_free = 0.3691 target = 0.115959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088746 restraints weight = 35019.634| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.28 r_work: 0.3170 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19312 Z= 0.106 Angle : 0.492 12.316 26367 Z= 0.235 Chirality : 0.037 0.305 3235 Planarity : 0.004 0.075 3282 Dihedral : 8.638 123.337 2854 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.71 % Allowed : 6.54 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.80 (0.19), residues: 2355 helix: 2.48 (0.14), residues: 1511 sheet: -0.19 (0.47), residues: 129 loop : -1.47 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 517 TYR 0.018 0.001 TYR A 998 PHE 0.014 0.001 PHE A 405 TRP 0.010 0.001 TRP A2221 HIS 0.008 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00238 (19311) covalent geometry : angle 0.49229 (26367) hydrogen bonds : bond 0.03692 ( 1179) hydrogen bonds : angle 3.23849 ( 3429) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 1465 HIS cc_start: 0.7098 (m-70) cc_final: 0.6864 (m-70) REVERT: A 1950 MET cc_start: 0.7129 (tmm) cc_final: 0.6866 (tmm) outliers start: 12 outliers final: 8 residues processed: 159 average time/residue: 0.1276 time to fit residues: 33.0345 Evaluate side-chains 150 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 79 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 256 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 152 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 248 optimal weight: 0.0370 chunk 69 optimal weight: 0.7980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1551 HIS B 159 ASN ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.115208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.087946 restraints weight = 35130.884| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.31 r_work: 0.3139 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19312 Z= 0.097 Angle : 0.441 8.452 26367 Z= 0.215 Chirality : 0.036 0.304 3235 Planarity : 0.004 0.065 3282 Dihedral : 8.506 124.717 2854 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.18 % Allowed : 8.48 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.18), residues: 2355 helix: 2.60 (0.14), residues: 1506 sheet: -0.07 (0.47), residues: 129 loop : -1.39 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 316 TYR 0.017 0.001 TYR A 998 PHE 0.015 0.001 PHE A 405 TRP 0.010 0.001 TRP A2221 HIS 0.007 0.001 HIS A1551 Details of bonding type rmsd covalent geometry : bond 0.00219 (19311) covalent geometry : angle 0.44057 (26367) hydrogen bonds : bond 0.03304 ( 1179) hydrogen bonds : angle 3.03913 ( 3429) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 1950 MET cc_start: 0.7118 (tmm) cc_final: 0.6840 (tmm) REVERT: B 415 TRP cc_start: 0.8454 (OUTLIER) cc_final: 0.7334 (t60) REVERT: C 517 ARG cc_start: 0.7885 (ptt-90) cc_final: 0.7224 (ptt-90) outliers start: 20 outliers final: 13 residues processed: 152 average time/residue: 0.1252 time to fit residues: 30.8810 Evaluate side-chains 151 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 1782 ASP Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2154 PHE Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3658 THR Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 170 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 145 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 989 ASN A1126 GLN A1551 HIS ** B 439 HIS ** 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 = 0.3642 r_free = 0.3642 target = 0.112675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.085374 restraints weight = 35276.462| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.32 r_work: 0.3082 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19312 Z= 0.136 Angle : 0.486 9.826 26367 Z= 0.238 Chirality : 0.037 0.325 3235 Planarity : 0.004 0.062 3282 Dihedral : 8.489 124.733 2854 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.77 % Allowed : 9.54 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.18), residues: 2355 helix: 2.53 (0.14), residues: 1500 sheet: 0.04 (0.47), residues: 129 loop : -1.39 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1443 TYR 0.016 0.001 TYR A 998 PHE 0.016 0.001 PHE A1827 TRP 0.008 0.001 TRP A2221 HIS 0.006 0.001 HIS A1551 Details of bonding type rmsd covalent geometry : bond 0.00329 (19311) covalent geometry : angle 0.48574 (26367) hydrogen bonds : bond 0.03924 ( 1179) hydrogen bonds : angle 3.10894 ( 3429) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.736 Fit side-chains REVERT: A 1950 MET cc_start: 0.7178 (tmm) cc_final: 0.6847 (tmm) REVERT: B 415 TRP cc_start: 0.8571 (OUTLIER) cc_final: 0.7379 (t60) REVERT: C 517 ARG cc_start: 0.7947 (ptt-90) cc_final: 0.7146 (ptt-90) outliers start: 30 outliers final: 18 residues processed: 157 average time/residue: 0.1228 time to fit residues: 31.6271 Evaluate side-chains 151 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1732 VAL Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2154 PHE Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3655 GLU Chi-restraints excluded: chain A residue 3658 THR Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 84 optimal weight: 0.5980 chunk 245 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 13 optimal weight: 30.0000 chunk 196 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 18 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 989 ASN ** B 439 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 = 0.3673 r_free = 0.3673 target = 0.114852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.087782 restraints weight = 34995.347| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.32 r_work: 0.3128 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19312 Z= 0.090 Angle : 0.438 8.833 26367 Z= 0.215 Chirality : 0.036 0.332 3235 Planarity : 0.003 0.060 3282 Dihedral : 8.355 124.137 2854 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.35 % Allowed : 10.72 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.18), residues: 2355 helix: 2.65 (0.14), residues: 1501 sheet: 0.19 (0.48), residues: 129 loop : -1.31 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 403 TYR 0.016 0.001 TYR A 998 PHE 0.012 0.001 PHE A 364 TRP 0.011 0.001 TRP A2221 HIS 0.003 0.000 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00202 (19311) covalent geometry : angle 0.43824 (26367) hydrogen bonds : bond 0.03101 ( 1179) hydrogen bonds : angle 2.97299 ( 3429) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.502 Fit side-chains REVERT: A 403 ARG cc_start: 0.7678 (tmm160) cc_final: 0.7394 (tmm160) REVERT: A 1204 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7376 (mm110) REVERT: A 1950 MET cc_start: 0.7162 (tmm) cc_final: 0.6837 (tmm) REVERT: B 415 TRP cc_start: 0.8482 (OUTLIER) cc_final: 0.7295 (t60) REVERT: C 517 ARG cc_start: 0.7901 (ptt-90) cc_final: 0.7637 (ptt-90) outliers start: 23 outliers final: 18 residues processed: 149 average time/residue: 0.1256 time to fit residues: 30.1768 Evaluate side-chains 152 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2154 PHE Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain A residue 3655 GLU Chi-restraints excluded: chain A residue 3658 THR Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 137 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 10 optimal weight: 40.0000 chunk 118 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 133 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 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 = 0.3663 r_free = 0.3663 target = 0.114161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.086756 restraints weight = 34947.050| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.31 r_work: 0.3119 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19312 Z= 0.100 Angle : 0.444 10.857 26367 Z= 0.217 Chirality : 0.036 0.335 3235 Planarity : 0.004 0.059 3282 Dihedral : 8.268 123.661 2854 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.77 % Allowed : 10.90 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.11 (0.18), residues: 2355 helix: 2.67 (0.14), residues: 1504 sheet: 0.28 (0.48), residues: 129 loop : -1.28 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1443 TYR 0.017 0.001 TYR A 998 PHE 0.016 0.001 PHE A 405 TRP 0.010 0.001 TRP A2221 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00236 (19311) covalent geometry : angle 0.44359 (26367) hydrogen bonds : bond 0.03215 ( 1179) hydrogen bonds : angle 2.95862 ( 3429) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.609 Fit side-chains REVERT: A 403 ARG cc_start: 0.7636 (tmm160) cc_final: 0.7315 (tmm160) REVERT: A 1950 MET cc_start: 0.7173 (tmm) cc_final: 0.6832 (tmm) REVERT: B 415 TRP cc_start: 0.8529 (OUTLIER) cc_final: 0.7371 (t60) outliers start: 30 outliers final: 22 residues processed: 150 average time/residue: 0.1261 time to fit residues: 30.6036 Evaluate side-chains 153 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1085 CYS Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2154 PHE Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain A residue 3655 GLU Chi-restraints excluded: chain A residue 3658 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 241 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 chunk 95 optimal weight: 0.0980 chunk 162 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 2 optimal weight: 50.0000 chunk 65 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 210 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 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 = 0.3642 r_free = 0.3642 target = 0.112498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.084980 restraints weight = 35254.931| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.25 r_work: 0.3105 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19312 Z= 0.108 Angle : 0.451 11.021 26367 Z= 0.221 Chirality : 0.036 0.336 3235 Planarity : 0.004 0.058 3282 Dihedral : 8.234 123.282 2854 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.53 % Allowed : 11.66 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.11 (0.18), residues: 2355 helix: 2.67 (0.14), residues: 1503 sheet: 0.29 (0.48), residues: 129 loop : -1.27 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2336 TYR 0.016 0.001 TYR A 998 PHE 0.016 0.001 PHE A 405 TRP 0.010 0.001 TRP A2221 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00259 (19311) covalent geometry : angle 0.45054 (26367) hydrogen bonds : bond 0.03336 ( 1179) hydrogen bonds : angle 2.97550 ( 3429) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 1950 MET cc_start: 0.7232 (tmm) cc_final: 0.6881 (tmm) REVERT: B 415 TRP cc_start: 0.8514 (OUTLIER) cc_final: 0.7385 (t60) outliers start: 26 outliers final: 23 residues processed: 144 average time/residue: 0.1270 time to fit residues: 29.8043 Evaluate side-chains 149 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1085 CYS Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain A residue 3655 GLU Chi-restraints excluded: chain A residue 3658 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 254 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 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 = 0.3628 r_free = 0.3628 target = 0.111540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.083989 restraints weight = 35228.926| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.26 r_work: 0.3085 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19312 Z= 0.122 Angle : 0.467 11.808 26367 Z= 0.229 Chirality : 0.037 0.336 3235 Planarity : 0.004 0.058 3282 Dihedral : 8.251 122.938 2854 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.88 % Allowed : 11.25 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.08 (0.18), residues: 2355 helix: 2.64 (0.14), residues: 1503 sheet: 0.29 (0.48), residues: 129 loop : -1.27 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 517 TYR 0.016 0.001 TYR A 998 PHE 0.016 0.001 PHE A 405 TRP 0.009 0.001 TRP A2221 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00294 (19311) covalent geometry : angle 0.46650 (26367) hydrogen bonds : bond 0.03565 ( 1179) hydrogen bonds : angle 3.02924 ( 3429) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 1950 MET cc_start: 0.7237 (tmm) cc_final: 0.6877 (tmm) REVERT: B 415 TRP cc_start: 0.8552 (OUTLIER) cc_final: 0.7424 (t60) REVERT: C 517 ARG cc_start: 0.7782 (ptt-90) cc_final: 0.7531 (ptt-90) outliers start: 32 outliers final: 28 residues processed: 147 average time/residue: 0.1333 time to fit residues: 31.9833 Evaluate side-chains 156 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1085 CYS Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1795 LEU Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain A residue 3655 GLU Chi-restraints excluded: chain A residue 3658 THR Chi-restraints excluded: chain A residue 3661 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 250 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 139 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 39 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 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 = 0.3670 r_free = 0.3670 target = 0.114746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.087531 restraints weight = 34852.365| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.30 r_work: 0.3126 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19312 Z= 0.086 Angle : 0.429 11.829 26367 Z= 0.211 Chirality : 0.035 0.334 3235 Planarity : 0.003 0.057 3282 Dihedral : 8.081 122.143 2854 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.94 % Allowed : 11.31 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.24 (0.18), residues: 2355 helix: 2.76 (0.14), residues: 1507 sheet: 0.40 (0.48), residues: 129 loop : -1.21 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 517 TYR 0.017 0.001 TYR A 998 PHE 0.018 0.001 PHE A 405 TRP 0.012 0.001 TRP A2221 HIS 0.003 0.000 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00192 (19311) covalent geometry : angle 0.42879 (26367) hydrogen bonds : bond 0.02840 ( 1179) hydrogen bonds : angle 2.90581 ( 3429) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 1950 MET cc_start: 0.7196 (tmm) cc_final: 0.6845 (tmm) REVERT: B 415 TRP cc_start: 0.8501 (OUTLIER) cc_final: 0.7368 (t60) outliers start: 33 outliers final: 25 residues processed: 152 average time/residue: 0.1242 time to fit residues: 30.9093 Evaluate side-chains 153 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1085 CYS Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1795 LEU Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain A residue 3658 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 67 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 225 optimal weight: 30.0000 chunk 253 optimal weight: 0.9990 chunk 130 optimal weight: 30.0000 chunk 190 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 989 ASN ** B 439 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 = 0.3608 r_free = 0.3608 target = 0.110118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.082710 restraints weight = 35241.508| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.23 r_work: 0.3065 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19312 Z= 0.149 Angle : 0.493 12.658 26367 Z= 0.243 Chirality : 0.038 0.346 3235 Planarity : 0.004 0.058 3282 Dihedral : 8.264 121.996 2854 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.65 % Allowed : 11.84 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.02 (0.18), residues: 2355 helix: 2.58 (0.14), residues: 1508 sheet: 0.33 (0.48), residues: 129 loop : -1.31 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 517 TYR 0.016 0.001 TYR A 998 PHE 0.020 0.001 PHE A 405 TRP 0.008 0.001 TRP A2221 HIS 0.004 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00364 (19311) covalent geometry : angle 0.49325 (26367) hydrogen bonds : bond 0.03976 ( 1179) hydrogen bonds : angle 3.08439 ( 3429) Misc. bond : bond 0.00019 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.533 Fit side-chains REVERT: A 1950 MET cc_start: 0.7268 (tmm) cc_final: 0.6887 (tmm) REVERT: B 415 TRP cc_start: 0.8643 (OUTLIER) cc_final: 0.7535 (t60) outliers start: 28 outliers final: 26 residues processed: 143 average time/residue: 0.1221 time to fit residues: 28.3250 Evaluate side-chains 151 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1085 CYS Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1795 LEU Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3655 GLU Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain A residue 3658 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 72 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 172 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 989 ASN ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 494 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.112778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085509 restraints weight = 35241.384| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.29 r_work: 0.3089 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19312 Z= 0.104 Angle : 0.460 12.481 26367 Z= 0.227 Chirality : 0.036 0.341 3235 Planarity : 0.004 0.057 3282 Dihedral : 8.180 121.699 2854 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.59 % Allowed : 11.96 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.18), residues: 2355 helix: 2.65 (0.14), residues: 1506 sheet: 0.36 (0.48), residues: 129 loop : -1.27 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 403 TYR 0.016 0.001 TYR A 998 PHE 0.011 0.001 PHE B 188 TRP 0.011 0.001 TRP A2221 HIS 0.004 0.001 HIS A2337 Details of bonding type rmsd covalent geometry : bond 0.00243 (19311) covalent geometry : angle 0.45962 (26367) hydrogen bonds : bond 0.03365 ( 1179) hydrogen bonds : angle 2.99290 ( 3429) Misc. bond : bond 0.00014 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5243.64 seconds wall clock time: 90 minutes 16.66 seconds (5416.66 seconds total)