Starting phenix.real_space_refine on Sat Mar 7 06:01:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zha_11217/03_2026/6zha_11217.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zha_11217/03_2026/6zha_11217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zha_11217/03_2026/6zha_11217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zha_11217/03_2026/6zha_11217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zha_11217/03_2026/6zha_11217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zha_11217/03_2026/6zha_11217.map" } resolution = 3.91 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= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 226 5.16 5 C 24410 2.51 5 N 6474 2.21 5 O 7133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s 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: 38289 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 28983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3679, 28983 Classifications: {'peptide': 3679} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 161, 'TRANS': 3517} Chain breaks: 14 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 635 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 13, 'ASN:plan1': 12, 'ASP:plan': 7, 'GLN:plan1': 8, 'PHE:plan': 6, 'TYR:plan': 4, 'HIS:plan': 2, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 307 Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 141 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 27} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3908 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 461} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 4260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4260 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 26, 'TRANS': 512} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 510 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "E" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 487 Inner-chain residues flagged as termini: ['pdbres=" DT E 35 "'] Classifications: {'DNA': 24} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 23} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {' DG:plan2': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 8.40, per 1000 atoms: 0.22 Number of scatterers: 38289 At special positions: 0 Unit cell: (137.55, 162.75, 223.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 226 16.00 P 46 15.00 O 7133 8.00 N 6474 7.00 C 24410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9078 Finding SS restraints... Warning! N2 atom is missing from residue DG E 29 Was trying to link: DC D 27 O2 with DG E 29 N2, Saenger class: 19 Warning! N2 atom is missing from residue DG E 29 Was trying to link: DC D 27 N3 with DG E 29 N2, Saenger class: 22 Warning! N2 atom is missing from residue DG E 29 Was trying to link: DC D 27 O2 with DG E 29 N2, Saenger class: 19 Warning! N2 atom is missing from residue DG E 29 Was trying to link: DC D 27 N3 with DG E 29 N2, Saenger class: 22 Warning! N2 atom is missing from residue DG E 29 Was trying to link: DC D 27 O2 with DG E 29 N2, Saenger class: 19 Warning! N2 atom is missing from residue DG E 29 Was trying to link: DC D 27 N3 with DG E 29 N2, Saenger class: 22 Warning! N2 atom is missing from residue DG E 29 Was trying to link: DC D 27 O2 with DG E 29 N2, Saenger class: 19 Warning! N2 atom is missing from residue DG E 29 Was trying to link: DC D 27 N3 with DG E 29 N2, Saenger class: 22 Secondary structure from input PDB file: 238 helices and 16 sheets defined 62.7% alpha, 4.2% beta 12 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 5.78 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 28 through 45 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.601A pdb=" N ASP A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 92 removed outlier: 3.753A pdb=" N GLU A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N CYS A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 116 Processing helix chain 'A' and resid 124 through 140 removed outlier: 3.500A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 162 removed outlier: 6.543A pdb=" N SER A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 186 through 208 removed outlier: 3.843A pdb=" N ASN A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 232 removed outlier: 3.749A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 256 removed outlier: 3.680A pdb=" N LEU A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.539A pdb=" N PHE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 291 through 302 Processing helix chain 'A' and resid 305 through 330 removed outlier: 4.568A pdb=" N ALA A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 removed outlier: 4.219A pdb=" N ILE A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.933A pdb=" N ILE A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 394 removed outlier: 3.517A pdb=" N VAL A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.698A pdb=" N TYR A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 409 through 424 removed outlier: 4.031A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 469 removed outlier: 3.744A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 3.823A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 removed outlier: 4.333A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 548 Processing helix chain 'A' and resid 559 through 579 removed outlier: 4.328A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 631 removed outlier: 3.614A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.786A pdb=" N PHE A 641 " --> pdb=" O GLN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 658 Processing helix chain 'A' and resid 663 through 680 removed outlier: 4.207A pdb=" N TYR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 through 759 removed outlier: 4.315A pdb=" N ALA A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.663A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 788 through 801 removed outlier: 3.601A pdb=" N ILE A 792 " --> pdb=" O TYR A 788 " (cutoff:3.500A) Proline residue: A 794 - end of helix removed outlier: 3.701A pdb=" N ASP A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR A 799 " --> pdb=" O CYS A 795 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 removed outlier: 3.768A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 868 removed outlier: 3.748A pdb=" N LYS A 868 " --> pdb=" O GLY A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 872 Processing helix chain 'A' and resid 876 through 882 removed outlier: 3.744A pdb=" N LYS A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 920 removed outlier: 3.930A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 946 Processing helix chain 'A' and resid 958 through 973 Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 977 through 996 removed outlier: 3.534A pdb=" N ARG A 981 " --> pdb=" O ASP A 977 " (cutoff:3.500A) Proline residue: A 986 - end of helix removed outlier: 3.555A pdb=" N MET A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1012 removed outlier: 3.600A pdb=" N LEU A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1038 removed outlier: 3.511A pdb=" N PHE A1028 " --> pdb=" O THR A1024 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1050 removed outlier: 3.629A pdb=" N GLU A1050 " --> pdb=" O PRO A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 removed outlier: 3.534A pdb=" N LYS A1061 " --> pdb=" O LYS A1057 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A1062 " --> pdb=" O SER A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1086 removed outlier: 3.616A pdb=" N ARG A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1115 removed outlier: 3.895A pdb=" N VAL A1105 " --> pdb=" O PHE A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1141 Processing helix chain 'A' and resid 1142 through 1147 removed outlier: 3.558A pdb=" N LYS A1147 " --> pdb=" O VAL A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1175 Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1212 Processing helix chain 'A' and resid 1215 through 1226 removed outlier: 4.281A pdb=" N ILE A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A1224 " --> pdb=" O LEU A1220 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A1225 " --> pdb=" O ILE A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1273 Processing helix chain 'A' and resid 1277 through 1282 Processing helix chain 'A' and resid 1289 through 1297 Processing helix chain 'A' and resid 1298 through 1300 No H-bonds generated for 'chain 'A' and resid 1298 through 1300' Processing helix chain 'A' and resid 1326 through 1350 Processing helix chain 'A' and resid 1360 through 1365 removed outlier: 3.819A pdb=" N LEU A1363 " --> pdb=" O LYS A1360 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN A1365 " --> pdb=" O ASP A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1378 removed outlier: 3.776A pdb=" N GLN A1374 " --> pdb=" O ARG A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1409 removed outlier: 3.989A pdb=" N ALA A1393 " --> pdb=" O VAL A1389 " (cutoff:3.500A) Proline residue: A1396 - end of helix removed outlier: 3.796A pdb=" N MET A1403 " --> pdb=" O CYS A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.618A pdb=" N LEU A1415 " --> pdb=" O TYR A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1435 removed outlier: 4.077A pdb=" N GLU A1430 " --> pdb=" O GLN A1426 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN A1435 " --> pdb=" O LEU A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1462 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.680A pdb=" N ILE A1467 " --> pdb=" O LEU A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1491 removed outlier: 4.614A pdb=" N GLU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A1484 " --> pdb=" O GLY A1480 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A1488 " --> pdb=" O LEU A1484 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A1489 " --> pdb=" O SER A1485 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1520 Processing helix chain 'A' and resid 1524 through 1533 Processing helix chain 'A' and resid 1555 through 1563 Processing helix chain 'A' and resid 1563 through 1574 Processing helix chain 'A' and resid 1574 through 1585 removed outlier: 4.057A pdb=" N ALA A1578 " --> pdb=" O ASN A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1607 removed outlier: 3.917A pdb=" N ASN A1598 " --> pdb=" O SER A1594 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1625 Processing helix chain 'A' and resid 1626 through 1629 removed outlier: 3.626A pdb=" N CYS A1629 " --> pdb=" O TRP A1626 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1626 through 1629' Processing helix chain 'A' and resid 1638 through 1655 removed outlier: 3.640A pdb=" N MET A1643 " --> pdb=" O LEU A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 3.596A pdb=" N VAL A1671 " --> pdb=" O SER A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1694 removed outlier: 3.729A pdb=" N THR A1694 " --> pdb=" O GLY A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1699 Processing helix chain 'A' and resid 1706 through 1722 removed outlier: 3.986A pdb=" N LEU A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1767 Processing helix chain 'A' and resid 1774 through 1786 removed outlier: 3.961A pdb=" N PHE A1778 " --> pdb=" O MET A1774 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 removed outlier: 4.729A pdb=" N MET A1804 " --> pdb=" O SER A1800 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE A1805 " --> pdb=" O VAL A1801 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A1806 " --> pdb=" O TYR A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 3.887A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1829 Processing helix chain 'A' and resid 1834 through 1853 removed outlier: 4.060A pdb=" N GLU A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE A1839 " --> pdb=" O ALA A1835 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A1853 " --> pdb=" O ASP A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1882 removed outlier: 3.842A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A1873 " --> pdb=" O LYS A1869 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A1879 " --> pdb=" O LYS A1875 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1924 removed outlier: 3.925A pdb=" N LYS A1917 " --> pdb=" O LYS A1913 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1955 Processing helix chain 'A' and resid 1970 through 1976 removed outlier: 3.722A pdb=" N ASN A1974 " --> pdb=" O LYS A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2106 removed outlier: 3.557A pdb=" N LEU A2097 " --> pdb=" O CYS A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2131 removed outlier: 4.252A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.965A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2161 through 2171 removed outlier: 4.166A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix removed outlier: 3.530A pdb=" N LEU A2171 " --> pdb=" O PRO A2167 " (cutoff:3.500A) Processing helix chain 'A' and resid 2185 through 2196 removed outlier: 3.765A pdb=" N TRP A2196 " --> pdb=" O THR A2192 " (cutoff:3.500A) Processing helix chain 'A' and resid 2208 through 2223 removed outlier: 3.949A pdb=" N HIS A2222 " --> pdb=" O PHE A2218 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2253 through 2261 removed outlier: 3.696A pdb=" N PHE A2257 " --> pdb=" O TYR A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2270 through 2283 removed outlier: 3.708A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2306 removed outlier: 3.841A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2309 No H-bonds generated for 'chain 'A' and resid 2307 through 2309' Processing helix chain 'A' and resid 2312 through 2329 removed outlier: 4.157A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR A2329 " --> pdb=" O LEU A2325 " (cutoff:3.500A) Processing helix chain 'A' and resid 2339 through 2350 removed outlier: 3.691A pdb=" N GLU A2343 " --> pdb=" O GLU A2339 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2369 removed outlier: 3.708A pdb=" N ILE A2361 " --> pdb=" O GLU A2357 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2373 Proline residue: A2373 - end of helix No H-bonds generated for 'chain 'A' and resid 2370 through 2373' Processing helix chain 'A' and resid 2374 through 2386 removed outlier: 3.967A pdb=" N PHE A2378 " --> pdb=" O LEU A2374 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN A2380 " --> pdb=" O ASP A2376 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA A2381 " --> pdb=" O ARG A2377 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.617A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2418 removed outlier: 4.327A pdb=" N GLN A2414 " --> pdb=" O GLU A2410 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A2418 " --> pdb=" O GLN A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2419 through 2426 removed outlier: 3.818A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2443 Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2456 removed outlier: 4.452A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A2454 " --> pdb=" O GLU A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2458 through 2462 removed outlier: 3.585A pdb=" N VAL A2462 " --> pdb=" O VAL A2459 " (cutoff:3.500A) Processing helix chain 'A' and resid 2468 through 2484 removed outlier: 3.560A pdb=" N ASN A2483 " --> pdb=" O TRP A2479 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2509 Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2514 through 2526 Processing helix chain 'A' and resid 2534 through 2543 removed outlier: 4.143A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2546 No H-bonds generated for 'chain 'A' and resid 2544 through 2546' Processing helix chain 'A' and resid 2547 through 2551 Processing helix chain 'A' and resid 2553 through 2564 Processing helix chain 'A' and resid 2565 through 2569 Processing helix chain 'A' and resid 2786 through 2799 removed outlier: 3.674A pdb=" N LEU A2790 " --> pdb=" O LYS A2786 " (cutoff:3.500A) Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2821 removed outlier: 3.582A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 Processing helix chain 'A' and resid 2851 through 2863 removed outlier: 3.721A pdb=" N SER A2862 " --> pdb=" O ILE A2858 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A2863 " --> pdb=" O GLN A2859 " (cutoff:3.500A) Processing helix chain 'A' and resid 2864 through 2869 removed outlier: 7.095A pdb=" N ALA A2867 " --> pdb=" O GLN A2864 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2882 Processing helix chain 'A' and resid 2885 through 2900 removed outlier: 3.751A pdb=" N LEU A2898 " --> pdb=" O GLU A2894 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A2900 " --> pdb=" O ALA A2896 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2934 Processing helix chain 'A' and resid 2936 through 2946 Processing helix chain 'A' and resid 2950 through 2962 removed outlier: 3.599A pdb=" N GLN A2954 " --> pdb=" O LYS A2950 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2977 removed outlier: 3.719A pdb=" N ALA A2968 " --> pdb=" O ASP A2964 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 Processing helix chain 'A' and resid 3007 through 3016 Processing helix chain 'A' and resid 3029 through 3033 Processing helix chain 'A' and resid 3035 through 3039 Processing helix chain 'A' and resid 3040 through 3056 removed outlier: 3.656A pdb=" N MET A3044 " --> pdb=" O TYR A3040 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A3056 " --> pdb=" O LEU A3052 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3069 Processing helix chain 'A' and resid 3071 through 3093 removed outlier: 3.669A pdb=" N LEU A3078 " --> pdb=" O GLN A3074 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU A3079 " --> pdb=" O LYS A3075 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS A3081 " --> pdb=" O ILE A3077 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLN A3084 " --> pdb=" O LEU A3080 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU A3085 " --> pdb=" O HIS A3081 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3117 removed outlier: 3.605A pdb=" N TYR A3101 " --> pdb=" O ASP A3097 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A3102 " --> pdb=" O ARG A3098 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A3117 " --> pdb=" O ASN A3113 " (cutoff:3.500A) Processing helix chain 'A' and resid 3121 through 3131 removed outlier: 3.770A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) Processing helix chain 'A' and resid 3132 through 3146 Processing helix chain 'A' and resid 3147 through 3153 Processing helix chain 'A' and resid 3154 through 3167 removed outlier: 3.628A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3194 removed outlier: 3.694A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A3194 " --> pdb=" O LEU A3190 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3249 removed outlier: 4.043A pdb=" N SER A3233 " --> pdb=" O SER A3229 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE A3243 " --> pdb=" O LYS A3239 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A3244 " --> pdb=" O MET A3240 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A3245 " --> pdb=" O LYS A3241 " (cutoff:3.500A) Processing helix chain 'A' and resid 3252 through 3262 removed outlier: 3.927A pdb=" N GLU A3261 " --> pdb=" O LYS A3257 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A3262 " --> pdb=" O LEU A3258 " (cutoff:3.500A) Processing helix chain 'A' and resid 3262 through 3267 removed outlier: 3.519A pdb=" N LYS A3267 " --> pdb=" O HIS A3263 " (cutoff:3.500A) Processing helix chain 'A' and resid 3270 through 3287 Processing helix chain 'A' and resid 3293 through 3306 removed outlier: 3.817A pdb=" N LEU A3306 " --> pdb=" O LYS A3302 " (cutoff:3.500A) Processing helix chain 'A' and resid 3313 through 3319 Processing helix chain 'A' and resid 3320 through 3344 Processing helix chain 'A' and resid 3358 through 3364 Processing helix chain 'A' and resid 3372 through 3394 removed outlier: 3.798A pdb=" N GLY A3376 " --> pdb=" O LYS A3372 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A3394 " --> pdb=" O GLN A3390 " (cutoff:3.500A) Processing helix chain 'A' and resid 3407 through 3427 removed outlier: 3.957A pdb=" N ASP A3411 " --> pdb=" O ALA A3407 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A3412 " --> pdb=" O GLY A3408 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.745A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3463 Processing helix chain 'A' and resid 3464 through 3473 removed outlier: 3.525A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3474 through 3480 removed outlier: 6.166A pdb=" N GLU A3477 " --> pdb=" O ARG A3474 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A3478 " --> pdb=" O TYR A3475 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A3479 " --> pdb=" O PRO A3476 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A3480 " --> pdb=" O GLU A3477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3474 through 3480' Processing helix chain 'A' and resid 3482 through 3488 removed outlier: 3.829A pdb=" N SER A3488 " --> pdb=" O THR A3484 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3506 Processing helix chain 'A' and resid 3511 through 3525 removed outlier: 4.004A pdb=" N SER A3517 " --> pdb=" O ALA A3513 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU A3520 " --> pdb=" O HIS A3516 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A3525 " --> pdb=" O ILE A3521 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3538 Processing helix chain 'A' and resid 3548 through 3562 removed outlier: 3.660A pdb=" N LYS A3552 " --> pdb=" O GLY A3548 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS A3559 " --> pdb=" O VAL A3555 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A3560 " --> pdb=" O ALA A3556 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A3561 " --> pdb=" O ARG A3557 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3579 Processing helix chain 'A' and resid 3580 through 3599 removed outlier: 3.918A pdb=" N THR A3599 " --> pdb=" O GLU A3595 " (cutoff:3.500A) Processing helix chain 'A' and resid 3605 through 3618 Processing helix chain 'A' and resid 3626 through 3637 removed outlier: 3.821A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A3635 " --> pdb=" O LYS A3631 " (cutoff:3.500A) Processing helix chain 'A' and resid 3638 through 3643 removed outlier: 3.829A pdb=" N HIS A3643 " --> pdb=" O GLU A3639 " (cutoff:3.500A) Processing helix chain 'A' and resid 3658 through 3669 removed outlier: 3.862A pdb=" N LYS A3669 " --> pdb=" O MET A3665 " (cutoff:3.500A) Processing helix chain 'A' and resid 3684 through 3689 Processing helix chain 'A' and resid 3758 through 3778 removed outlier: 3.702A pdb=" N GLY A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) Processing helix chain 'A' and resid 3779 through 3784 removed outlier: 3.937A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 3.637A pdb=" N ASN A3818 " --> pdb=" O ASP A3814 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3847 Processing helix chain 'A' and resid 3853 through 3862 removed outlier: 3.502A pdb=" N LEU A3857 " --> pdb=" O GLY A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3878 removed outlier: 3.654A pdb=" N LYS A3873 " --> pdb=" O THR A3869 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A3878 " --> pdb=" O ARG A3874 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3890 Processing helix chain 'A' and resid 3893 through 3919 Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3947 through 3952 Processing helix chain 'A' and resid 3964 through 3969 Processing helix chain 'A' and resid 3978 through 3993 Processing helix chain 'A' and resid 3994 through 4008 removed outlier: 4.469A pdb=" N LEU A3998 " --> pdb=" O ASP A3994 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A4000 " --> pdb=" O GLY A3996 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A4004 " --> pdb=" O ASN A4000 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A4005 " --> pdb=" O THR A4001 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A4006 " --> pdb=" O MET A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4011 No H-bonds generated for 'chain 'A' and resid 4009 through 4011' Processing helix chain 'A' and resid 4012 through 4021 Processing helix chain 'A' and resid 4039 through 4051 removed outlier: 4.297A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4069 removed outlier: 3.627A pdb=" N LEU A4065 " --> pdb=" O CYS A4061 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A4066 " --> pdb=" O ASP A4062 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A4067 " --> pdb=" O GLU A4063 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A4069 " --> pdb=" O LEU A4065 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4082 removed outlier: 3.834A pdb=" N VAL A4080 " --> pdb=" O ASP A4076 " (cutoff:3.500A) Processing helix chain 'A' and resid 4088 through 4092 Processing helix chain 'A' and resid 4099 through 4112 removed outlier: 3.712A pdb=" N VAL A4104 " --> pdb=" O GLU A4100 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS A4105 " --> pdb=" O GLU A4101 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4121 through 4125 removed outlier: 3.508A pdb=" N GLU A4125 " --> pdb=" O GLU A4122 " (cutoff:3.500A) Processing helix chain 'A' and resid 5012 through 5016 removed outlier: 4.269A pdb=" N UNK A5016 " --> pdb=" O UNK A5013 " (cutoff:3.500A) Processing helix chain 'A' and resid 6005 through 6017 removed outlier: 3.686A pdb=" N UNK A6011 " --> pdb=" O UNK A6007 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N UNK A6015 " --> pdb=" O UNK A6011 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK A6017 " --> pdb=" O UNK A6013 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 76 removed outlier: 3.644A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 121 removed outlier: 3.556A pdb=" N ILE B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 135 removed outlier: 3.818A pdb=" N ASP B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 156 Processing helix chain 'B' and resid 179 through 197 removed outlier: 3.588A pdb=" N ALA B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 4.087A pdb=" N ASP B 219 " --> pdb=" O PHE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.687A pdb=" N LEU B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.890A pdb=" N LEU B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 removed outlier: 3.580A pdb=" N LYS B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 455 through 468 removed outlier: 3.704A pdb=" N VAL B 459 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 removed outlier: 3.636A pdb=" N GLN B 484 " --> pdb=" O ASN B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 519 removed outlier: 5.200A pdb=" N LYS B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 4.096A pdb=" N GLU B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 48 Processing helix chain 'C' and resid 87 through 96 removed outlier: 3.910A pdb=" N LEU C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 121 Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 198 through 216 Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.876A pdb=" N LEU C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.594A pdb=" N LYS C 239 " --> pdb=" O CYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 332 removed outlier: 4.001A pdb=" N GLN C 330 " --> pdb=" O VAL C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 370 through 388 Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 484 through 500 removed outlier: 4.242A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 517 Processing helix chain 'C' and resid 519 through 537 removed outlier: 3.864A pdb=" N THR C 523 " --> pdb=" O PRO C 519 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 1537 through 1538 Processing sheet with id=AA4, first strand: chain 'A' and resid 2586 through 2587 Processing sheet with id=AA5, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 5.995A pdb=" N ARG A3741 " --> pdb=" O ALA A3720 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE A3722 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE A3739 " --> pdb=" O PHE A3722 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 5.995A pdb=" N ARG A3741 " --> pdb=" O ALA A3720 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE A3722 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE A3739 " --> pdb=" O PHE A3722 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3928 through 3930 Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 109 removed outlier: 6.580A pdb=" N VAL B 85 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU B 107 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU B 83 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 260 through 262 removed outlier: 3.556A pdb=" N ILE B 269 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 432 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 396 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA B 395 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE B 350 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 397 " --> pdb=" O MET B 348 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 344 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LYS B 260 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU B 347 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS B 262 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLY B 349 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 286 through 287 Processing sheet with id=AB2, first strand: chain 'B' and resid 300 through 303 Processing sheet with id=AB3, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB4, first strand: chain 'C' and resid 77 through 84 removed outlier: 6.244A pdb=" N LEU C 56 " --> pdb=" O HIS C 80 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N HIS C 82 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE C 54 " --> pdb=" O HIS C 82 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 11 " --> pdb=" O HIS C 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 249 through 250 removed outlier: 7.937A pdb=" N GLN C 360 " --> pdb=" O GLN C 423 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLN C 423 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 419 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL C 405 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N MET C 389 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL C 390 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE C 345 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE C 392 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER C 341 " --> pdb=" O ARG C 394 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.903A pdb=" N THR C 303 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 464 through 467 removed outlier: 3.603A pdb=" N GLU C 474 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP C 467 " --> pdb=" O THR C 472 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR C 472 " --> pdb=" O ASP C 467 " (cutoff:3.500A) 1888 hydrogen bonds defined for protein. 5535 hydrogen bond angles defined for protein. NA hbond rejected because one of the atoms is absent Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 14.59 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7837 1.33 - 1.45: 8753 1.45 - 1.57: 22122 1.57 - 1.69: 93 1.69 - 1.81: 357 Bond restraints: 39162 Sorted by residual: bond pdb=" C ARG A3734 " pdb=" O ARG A3734 " ideal model delta sigma weight residual 1.235 1.215 0.020 4.70e-03 4.53e+04 1.77e+01 bond pdb=" CA PRO A1730 " pdb=" C PRO A1730 " ideal model delta sigma weight residual 1.517 1.498 0.019 6.70e-03 2.23e+04 7.82e+00 bond pdb=" CB MET A1757 " pdb=" CG MET A1757 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.37e+00 bond pdb=" CA GLU A1607 " pdb=" CB GLU A1607 " ideal model delta sigma weight residual 1.528 1.470 0.059 2.61e-02 1.47e+03 5.07e+00 bond pdb=" N ASP A3673 " pdb=" CA ASP A3673 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.46e+00 ... (remaining 39157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 51698 2.29 - 4.57: 1251 4.57 - 6.86: 187 6.86 - 9.15: 31 9.15 - 11.43: 12 Bond angle restraints: 53179 Sorted by residual: angle pdb=" N GLN A2351 " pdb=" CA GLN A2351 " pdb=" C GLN A2351 " ideal model delta sigma weight residual 111.40 100.98 10.42 1.22e+00 6.72e-01 7.29e+01 angle pdb=" N ASN A3671 " pdb=" CA ASN A3671 " pdb=" C ASN A3671 " ideal model delta sigma weight residual 112.04 100.61 11.43 1.44e+00 4.82e-01 6.30e+01 angle pdb=" N ILE A4028 " pdb=" CA ILE A4028 " pdb=" C ILE A4028 " ideal model delta sigma weight residual 112.43 105.33 7.10 9.20e-01 1.18e+00 5.95e+01 angle pdb=" N PRO A 126 " pdb=" CA PRO A 126 " pdb=" CB PRO A 126 " ideal model delta sigma weight residual 103.39 110.76 -7.37 1.08e+00 8.57e-01 4.65e+01 angle pdb=" N VAL A2330 " pdb=" CA VAL A2330 " pdb=" C VAL A2330 " ideal model delta sigma weight residual 109.34 119.82 -10.48 2.08e+00 2.31e-01 2.54e+01 ... (remaining 53174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 21004 17.96 - 35.93: 2190 35.93 - 53.89: 469 53.89 - 71.85: 118 71.85 - 89.82: 42 Dihedral angle restraints: 23823 sinusoidal: 9897 harmonic: 13926 Sorted by residual: dihedral pdb=" CA TYR A1086 " pdb=" C TYR A1086 " pdb=" N ARG A1087 " pdb=" CA ARG A1087 " ideal model delta harmonic sigma weight residual 180.00 -151.11 -28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLU A1299 " pdb=" C GLU A1299 " pdb=" N SER A1300 " pdb=" CA SER A1300 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LEU A1014 " pdb=" C LEU A1014 " pdb=" N ASP A1015 " pdb=" CA ASP A1015 " ideal model delta harmonic sigma weight residual 180.00 151.57 28.43 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 23820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4685 0.055 - 0.109: 1241 0.109 - 0.164: 121 0.164 - 0.218: 10 0.218 - 0.273: 6 Chirality restraints: 6063 Sorted by residual: chirality pdb=" CA ASN A3671 " pdb=" N ASN A3671 " pdb=" C ASN A3671 " pdb=" CB ASN A3671 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB ILE A1013 " pdb=" CA ILE A1013 " pdb=" CG1 ILE A1013 " pdb=" CG2 ILE A1013 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TYR A 265 " pdb=" N TYR A 265 " pdb=" C TYR A 265 " pdb=" CB TYR A 265 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 6060 not shown) Planarity restraints: 6617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A3831 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO A3832 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO A3832 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A3832 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1389 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C VAL A1389 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL A1389 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN A1390 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 66 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO C 67 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 67 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 67 " 0.047 5.00e-02 4.00e+02 ... (remaining 6614 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 4324 2.73 - 3.27: 45488 3.27 - 3.81: 65801 3.81 - 4.36: 79142 4.36 - 4.90: 123800 Nonbonded interactions: 318555 Sorted by model distance: nonbonded pdb=" NZ LYS A3710 " pdb=" O PRO A3711 " model vdw 2.183 3.120 nonbonded pdb=" O ARG A1321 " pdb=" NH1 ARG A1321 " model vdw 2.184 3.120 nonbonded pdb=" O ILE A1414 " pdb=" ND1 HIS A1418 " model vdw 2.198 3.120 nonbonded pdb=" O GLN A3059 " pdb=" OG1 THR A3063 " model vdw 2.199 3.040 nonbonded pdb=" OG SER A3288 " pdb=" NH1 ARG A3289 " model vdw 2.199 3.120 ... (remaining 318550 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.500 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 46.130 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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 : 0.008 0.100 39162 Z= 0.378 Angle : 0.889 11.432 53179 Z= 0.481 Chirality : 0.046 0.273 6063 Planarity : 0.005 0.122 6617 Dihedral : 15.856 89.818 14745 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.60 % Favored : 90.23 % Rotamer: Outliers : 0.10 % Allowed : 0.67 % Favored : 99.23 % Cbeta Deviations : 0.02 % 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: -2.01 (0.12), residues: 4669 helix: -0.60 (0.10), residues: 2534 sheet: -1.01 (0.36), residues: 188 loop : -2.33 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1711 TYR 0.039 0.002 TYR A3610 PHE 0.031 0.002 PHE A 200 TRP 0.030 0.003 TRP A2981 HIS 0.008 0.002 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00773 (39162) covalent geometry : angle 0.88938 (53179) hydrogen bonds : bond 0.19624 ( 1912) hydrogen bonds : angle 7.53605 ( 5585) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 158 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.7643 (ppp) cc_final: 0.7046 (ppp) REVERT: A 441 MET cc_start: 0.9023 (mmt) cc_final: 0.8738 (tmm) REVERT: A 540 MET cc_start: 0.9303 (mpp) cc_final: 0.9052 (mpp) REVERT: A 754 MET cc_start: 0.9159 (tpp) cc_final: 0.8849 (tpp) REVERT: A 1600 MET cc_start: 0.9433 (tpp) cc_final: 0.9134 (tpt) REVERT: A 1643 MET cc_start: 0.9088 (mpp) cc_final: 0.8771 (mpp) REVERT: A 1762 MET cc_start: 0.9627 (mmm) cc_final: 0.9343 (mmm) REVERT: A 1774 MET cc_start: 0.9512 (mmp) cc_final: 0.9289 (mmm) REVERT: A 1871 MET cc_start: 0.9660 (mtp) cc_final: 0.9291 (mtp) REVERT: A 2478 MET cc_start: 0.9279 (mtm) cc_final: 0.9063 (mtm) REVERT: A 2565 MET cc_start: 0.8761 (tpp) cc_final: 0.8483 (tpp) REVERT: A 3173 MET cc_start: 0.8835 (tpp) cc_final: 0.8455 (tpp) REVERT: A 3687 MET cc_start: 0.9179 (mtt) cc_final: 0.8889 (mtt) REVERT: A 3820 MET cc_start: 0.8306 (ppp) cc_final: 0.7890 (ppp) REVERT: B 48 MET cc_start: 0.9331 (pmm) cc_final: 0.8817 (pmm) REVERT: B 266 ASP cc_start: 0.9437 (m-30) cc_final: 0.9179 (t70) REVERT: B 346 MET cc_start: 0.9215 (tpt) cc_final: 0.8904 (tpt) REVERT: B 462 MET cc_start: 0.8875 (mpp) cc_final: 0.8235 (mpp) outliers start: 4 outliers final: 1 residues processed: 161 average time/residue: 0.2154 time to fit residues: 60.1300 Evaluate side-chains 150 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1356 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.1980 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 470 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN A 325 ASN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 ASN A2365 ASN A2859 GLN ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN C 547 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.034843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.025265 restraints weight = 399900.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.026077 restraints weight = 233190.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.026624 restraints weight = 162807.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.027002 restraints weight = 127291.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.027235 restraints weight = 107044.967| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 39162 Z= 0.165 Angle : 0.695 10.581 53179 Z= 0.361 Chirality : 0.042 0.184 6063 Planarity : 0.005 0.074 6617 Dihedral : 12.760 88.475 5627 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.22 % Allowed : 7.45 % Favored : 92.32 % 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: -1.29 (0.12), residues: 4669 helix: 0.05 (0.10), residues: 2612 sheet: -0.79 (0.39), residues: 169 loop : -2.16 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1711 TYR 0.034 0.002 TYR A3610 PHE 0.027 0.002 PHE A2260 TRP 0.014 0.001 TRP A3031 HIS 0.009 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00354 (39162) covalent geometry : angle 0.69525 (53179) hydrogen bonds : bond 0.04892 ( 1912) hydrogen bonds : angle 5.31927 ( 5585) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.9140 (tmm) cc_final: 0.8844 (ppp) REVERT: A 342 MET cc_start: 0.7618 (ppp) cc_final: 0.7008 (ppp) REVERT: A 540 MET cc_start: 0.9241 (mpp) cc_final: 0.8969 (mpp) REVERT: A 602 MET cc_start: 0.8708 (mmt) cc_final: 0.8399 (tpt) REVERT: A 754 MET cc_start: 0.9127 (tpp) cc_final: 0.8737 (tpp) REVERT: A 785 MET cc_start: 0.9005 (mpp) cc_final: 0.8738 (mpp) REVERT: A 1600 MET cc_start: 0.9224 (tpp) cc_final: 0.8934 (tpt) REVERT: A 1762 MET cc_start: 0.9520 (mmm) cc_final: 0.9309 (mmm) REVERT: A 1774 MET cc_start: 0.9330 (mmp) cc_final: 0.9085 (mmm) REVERT: A 2415 LEU cc_start: 0.9754 (tp) cc_final: 0.9543 (tp) REVERT: A 2473 MET cc_start: 0.9522 (ttp) cc_final: 0.9303 (ttp) REVERT: A 2478 MET cc_start: 0.9159 (mtm) cc_final: 0.8918 (mtm) REVERT: A 3111 MET cc_start: 0.8976 (pmm) cc_final: 0.8553 (pmm) REVERT: A 3173 MET cc_start: 0.8550 (tpp) cc_final: 0.8083 (tpp) REVERT: A 3483 MET cc_start: 0.8644 (ttp) cc_final: 0.8413 (ptm) REVERT: A 3687 MET cc_start: 0.9113 (mtt) cc_final: 0.8819 (mtt) REVERT: A 3820 MET cc_start: 0.8552 (ppp) cc_final: 0.8279 (ppp) REVERT: B 48 MET cc_start: 0.9204 (pmm) cc_final: 0.8387 (pmm) REVERT: B 346 MET cc_start: 0.9214 (tpt) cc_final: 0.8843 (tpt) REVERT: C 461 MET cc_start: 0.8163 (ppp) cc_final: 0.7856 (ppp) outliers start: 9 outliers final: 3 residues processed: 168 average time/residue: 0.2160 time to fit residues: 63.4584 Evaluate side-chains 153 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 2438 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 215 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 264 optimal weight: 3.9990 chunk 452 optimal weight: 20.0000 chunk 340 optimal weight: 5.9990 chunk 406 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 379 optimal weight: 20.0000 chunk 353 optimal weight: 6.9990 chunk 383 optimal weight: 0.0980 chunk 411 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN A3133 GLN ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4029 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.034857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.025353 restraints weight = 397961.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.026164 restraints weight = 233153.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.026707 restraints weight = 162875.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.027065 restraints weight = 127411.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.027333 restraints weight = 107712.264| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39162 Z= 0.149 Angle : 0.627 9.950 53179 Z= 0.326 Chirality : 0.040 0.182 6063 Planarity : 0.004 0.062 6617 Dihedral : 12.561 88.469 5625 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.52 % Allowed : 10.66 % Favored : 88.82 % 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: -0.97 (0.13), residues: 4669 helix: 0.33 (0.10), residues: 2647 sheet: -0.92 (0.36), residues: 193 loop : -2.07 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3380 TYR 0.030 0.001 TYR A3610 PHE 0.021 0.001 PHE A2260 TRP 0.014 0.001 TRP A1356 HIS 0.006 0.001 HIS A3070 Details of bonding type rmsd covalent geometry : bond 0.00318 (39162) covalent geometry : angle 0.62717 (53179) hydrogen bonds : bond 0.04255 ( 1912) hydrogen bonds : angle 4.93013 ( 5585) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8181 (tp) REVERT: A 342 MET cc_start: 0.7634 (ppp) cc_final: 0.6961 (ppp) REVERT: A 410 MET cc_start: 0.9544 (mmm) cc_final: 0.9313 (mmm) REVERT: A 540 MET cc_start: 0.9255 (mpp) cc_final: 0.9008 (mpp) REVERT: A 718 MET cc_start: 0.8975 (ppp) cc_final: 0.8747 (ppp) REVERT: A 754 MET cc_start: 0.9136 (tpp) cc_final: 0.8697 (tpp) REVERT: A 785 MET cc_start: 0.8931 (mpp) cc_final: 0.8505 (mpp) REVERT: A 1600 MET cc_start: 0.9136 (tpp) cc_final: 0.8740 (tpt) REVERT: A 1643 MET cc_start: 0.9061 (mpp) cc_final: 0.8809 (mpp) REVERT: A 2274 ILE cc_start: 0.9761 (mm) cc_final: 0.9431 (tp) REVERT: A 2473 MET cc_start: 0.9522 (ttp) cc_final: 0.9295 (ttp) REVERT: A 2478 MET cc_start: 0.9144 (mtm) cc_final: 0.8938 (mtm) REVERT: A 3111 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8669 (pmm) REVERT: A 3173 MET cc_start: 0.8552 (tpp) cc_final: 0.8044 (tpp) REVERT: A 3240 MET cc_start: 0.9202 (tpp) cc_final: 0.8996 (tpp) REVERT: A 3687 MET cc_start: 0.9197 (mtt) cc_final: 0.8856 (mtt) REVERT: A 3820 MET cc_start: 0.8565 (ppp) cc_final: 0.8281 (ppp) REVERT: A 3984 MET cc_start: 0.9041 (mtm) cc_final: 0.8829 (mtm) REVERT: A 4029 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: B 48 MET cc_start: 0.9207 (pmm) cc_final: 0.8414 (pmm) REVERT: B 346 MET cc_start: 0.9250 (tpt) cc_final: 0.9016 (tpt) REVERT: C 14 MET cc_start: 0.9203 (ppp) cc_final: 0.8885 (pmm) outliers start: 21 outliers final: 6 residues processed: 169 average time/residue: 0.1990 time to fit residues: 59.7224 Evaluate side-chains 156 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 2933 ILE Chi-restraints excluded: chain A residue 3111 MET Chi-restraints excluded: chain A residue 4029 GLN Chi-restraints excluded: chain B residue 267 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 116 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 304 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 257 optimal weight: 0.7980 chunk 337 optimal weight: 10.0000 chunk 207 optimal weight: 0.6980 chunk 442 optimal weight: 9.9990 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 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 HIS A 753 GLN A1687 HIS A2217 ASN A2859 GLN ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4029 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.035158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.025751 restraints weight = 391805.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.026565 restraints weight = 229628.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.027114 restraints weight = 160222.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.027486 restraints weight = 124848.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.027749 restraints weight = 104995.020| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39162 Z= 0.118 Angle : 0.605 9.440 53179 Z= 0.311 Chirality : 0.040 0.186 6063 Planarity : 0.004 0.053 6617 Dihedral : 12.429 86.858 5625 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.94 % Allowed : 12.44 % Favored : 86.62 % 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: -0.73 (0.13), residues: 4669 helix: 0.56 (0.10), residues: 2650 sheet: -0.78 (0.37), residues: 193 loop : -2.03 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.027 0.001 TYR A3610 PHE 0.022 0.001 PHE A2260 TRP 0.013 0.001 TRP A1633 HIS 0.004 0.001 HIS A1367 Details of bonding type rmsd covalent geometry : bond 0.00253 (39162) covalent geometry : angle 0.60524 (53179) hydrogen bonds : bond 0.03751 ( 1912) hydrogen bonds : angle 4.66051 ( 5585) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9536 (OUTLIER) cc_final: 0.9288 (pm20) REVERT: A 144 MET cc_start: 0.8949 (tmm) cc_final: 0.8511 (ppp) REVERT: A 342 MET cc_start: 0.7514 (ppp) cc_final: 0.6875 (ppp) REVERT: A 366 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8648 (t80) REVERT: A 540 MET cc_start: 0.9214 (mpp) cc_final: 0.9002 (mpp) REVERT: A 718 MET cc_start: 0.8944 (ppp) cc_final: 0.8707 (ppp) REVERT: A 754 MET cc_start: 0.9149 (tpp) cc_final: 0.8686 (tpp) REVERT: A 1404 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9076 (mmtm) REVERT: A 1600 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8720 (tpt) REVERT: A 1743 MET cc_start: 0.9614 (OUTLIER) cc_final: 0.8998 (mmt) REVERT: A 1825 LEU cc_start: 0.9723 (tt) cc_final: 0.9490 (mt) REVERT: A 2274 ILE cc_start: 0.9752 (mm) cc_final: 0.9476 (tp) REVERT: A 2279 ILE cc_start: 0.8785 (mm) cc_final: 0.8579 (mm) REVERT: A 2478 MET cc_start: 0.9166 (mtm) cc_final: 0.8953 (mtm) REVERT: A 3111 MET cc_start: 0.8949 (pmm) cc_final: 0.8672 (pmm) REVERT: A 3173 MET cc_start: 0.8507 (tpp) cc_final: 0.7991 (tpp) REVERT: A 3654 MET cc_start: 0.4497 (pmm) cc_final: 0.4060 (pmm) REVERT: A 3687 MET cc_start: 0.9228 (mtt) cc_final: 0.8796 (mtt) REVERT: A 3820 MET cc_start: 0.8605 (ppp) cc_final: 0.8349 (ppp) REVERT: A 3984 MET cc_start: 0.9135 (mtm) cc_final: 0.8884 (mtm) REVERT: A 4029 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: B 38 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8231 (tt) REVERT: B 48 MET cc_start: 0.9168 (pmm) cc_final: 0.8336 (pmm) REVERT: B 346 MET cc_start: 0.9301 (tpt) cc_final: 0.9076 (tpt) REVERT: C 14 MET cc_start: 0.9180 (ppp) cc_final: 0.8781 (pmm) REVERT: C 389 MET cc_start: 0.7741 (mmm) cc_final: 0.6454 (mmm) REVERT: C 461 MET cc_start: 0.8185 (ppp) cc_final: 0.7943 (ppp) outliers start: 38 outliers final: 13 residues processed: 186 average time/residue: 0.2061 time to fit residues: 68.3929 Evaluate side-chains 170 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1404 LYS Chi-restraints excluded: chain A residue 1600 MET Chi-restraints excluded: chain A residue 1743 MET Chi-restraints excluded: chain A residue 2438 ILE Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4029 GLN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 11 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 10.0000 chunk 173 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 425 optimal weight: 0.8980 chunk 304 optimal weight: 8.9990 chunk 446 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 299 optimal weight: 0.0370 chunk 260 optimal weight: 9.9990 overall best weight: 2.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1320 ASN A2859 GLN ** A3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3924 HIS ** A4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.035133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.025694 restraints weight = 396641.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.026508 restraints weight = 232525.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.027051 restraints weight = 162296.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.027431 restraints weight = 126804.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.027686 restraints weight = 106466.520| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39162 Z= 0.129 Angle : 0.600 9.301 53179 Z= 0.308 Chirality : 0.040 0.180 6063 Planarity : 0.004 0.052 6617 Dihedral : 12.305 86.072 5625 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.16 % Allowed : 13.72 % Favored : 85.12 % 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: -0.57 (0.13), residues: 4669 helix: 0.70 (0.10), residues: 2645 sheet: -0.68 (0.38), residues: 185 loop : -1.98 (0.15), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.024 0.001 TYR A3610 PHE 0.020 0.001 PHE A2260 TRP 0.014 0.001 TRP A1633 HIS 0.003 0.001 HIS A3070 Details of bonding type rmsd covalent geometry : bond 0.00277 (39162) covalent geometry : angle 0.60036 (53179) hydrogen bonds : bond 0.03616 ( 1912) hydrogen bonds : angle 4.55310 ( 5585) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9564 (OUTLIER) cc_final: 0.9292 (pm20) REVERT: A 96 MET cc_start: 0.2166 (OUTLIER) cc_final: 0.0399 (mtm) REVERT: A 342 MET cc_start: 0.7536 (ppp) cc_final: 0.6881 (ppp) REVERT: A 366 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8743 (t80) REVERT: A 395 MET cc_start: 0.8895 (tpp) cc_final: 0.8646 (tpp) REVERT: A 540 MET cc_start: 0.9228 (mpp) cc_final: 0.9020 (mpp) REVERT: A 718 MET cc_start: 0.8939 (ppp) cc_final: 0.8695 (ppp) REVERT: A 754 MET cc_start: 0.9160 (tpp) cc_final: 0.8531 (tpp) REVERT: A 939 MET cc_start: 0.9217 (mmm) cc_final: 0.8938 (mmm) REVERT: A 1108 MET cc_start: 0.9351 (ttm) cc_final: 0.9122 (ttt) REVERT: A 1404 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9135 (mmtm) REVERT: A 1643 MET cc_start: 0.9002 (mpp) cc_final: 0.8749 (mpp) REVERT: A 1743 MET cc_start: 0.9565 (OUTLIER) cc_final: 0.9008 (mmt) REVERT: A 1762 MET cc_start: 0.9475 (mmm) cc_final: 0.9114 (mmm) REVERT: A 2274 ILE cc_start: 0.9750 (mm) cc_final: 0.9482 (tp) REVERT: A 2279 ILE cc_start: 0.8779 (mm) cc_final: 0.8568 (mm) REVERT: A 2473 MET cc_start: 0.9489 (ttp) cc_final: 0.9264 (ttp) REVERT: A 2478 MET cc_start: 0.9148 (mtm) cc_final: 0.8931 (mtm) REVERT: A 3111 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8637 (pmm) REVERT: A 3173 MET cc_start: 0.8505 (tpp) cc_final: 0.8003 (tpp) REVERT: A 3240 MET cc_start: 0.9152 (tpp) cc_final: 0.8905 (tpp) REVERT: A 3687 MET cc_start: 0.9269 (mtt) cc_final: 0.8777 (mtt) REVERT: A 3820 MET cc_start: 0.8614 (ppp) cc_final: 0.8399 (ppp) REVERT: A 3984 MET cc_start: 0.9141 (mtm) cc_final: 0.8886 (mtm) REVERT: B 38 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8107 (tt) REVERT: B 48 MET cc_start: 0.9177 (pmm) cc_final: 0.8363 (pmm) REVERT: B 161 MET cc_start: 0.8426 (mmm) cc_final: 0.7832 (mmm) REVERT: B 346 MET cc_start: 0.9309 (tpt) cc_final: 0.9094 (tpt) REVERT: C 389 MET cc_start: 0.7944 (mmm) cc_final: 0.7634 (mmm) REVERT: C 515 MET cc_start: 0.9710 (ptp) cc_final: 0.9510 (ptp) outliers start: 47 outliers final: 15 residues processed: 190 average time/residue: 0.2125 time to fit residues: 71.3984 Evaluate side-chains 173 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1404 LYS Chi-restraints excluded: chain A residue 1743 MET Chi-restraints excluded: chain A residue 2221 LYS Chi-restraints excluded: chain A residue 3111 MET Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 11 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 297 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 435 optimal weight: 30.0000 chunk 280 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 328 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 401 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2553 HIS A3074 GLN ** A3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3422 GLN ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.034183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.024775 restraints weight = 406206.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.025564 restraints weight = 234950.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.026106 restraints weight = 163380.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.026481 restraints weight = 127009.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.026716 restraints weight = 106420.317| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 39162 Z= 0.221 Angle : 0.668 15.520 53179 Z= 0.340 Chirality : 0.041 0.226 6063 Planarity : 0.004 0.053 6617 Dihedral : 12.270 85.645 5625 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.81 % Allowed : 14.81 % Favored : 84.38 % 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: -0.59 (0.13), residues: 4669 helix: 0.66 (0.10), residues: 2642 sheet: -0.78 (0.37), residues: 189 loop : -1.94 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.023 0.001 TYR A3610 PHE 0.017 0.002 PHE A1563 TRP 0.016 0.001 TRP A3916 HIS 0.004 0.001 HIS A1476 Details of bonding type rmsd covalent geometry : bond 0.00466 (39162) covalent geometry : angle 0.66818 (53179) hydrogen bonds : bond 0.03852 ( 1912) hydrogen bonds : angle 4.67993 ( 5585) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.2249 (OUTLIER) cc_final: 0.0478 (mtm) REVERT: A 342 MET cc_start: 0.7581 (ppp) cc_final: 0.6934 (ppp) REVERT: A 366 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8785 (t80) REVERT: A 395 MET cc_start: 0.9145 (tpp) cc_final: 0.8822 (tpp) REVERT: A 540 MET cc_start: 0.9326 (mpp) cc_final: 0.9068 (mpp) REVERT: A 718 MET cc_start: 0.9058 (ppp) cc_final: 0.8802 (ppp) REVERT: A 754 MET cc_start: 0.9197 (tpp) cc_final: 0.8575 (tpp) REVERT: A 939 MET cc_start: 0.9323 (mmm) cc_final: 0.9069 (mmm) REVERT: A 1108 MET cc_start: 0.9393 (ttm) cc_final: 0.9142 (ttt) REVERT: A 1404 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.9130 (mmtm) REVERT: A 1583 MET cc_start: 0.8127 (tpt) cc_final: 0.7910 (tpt) REVERT: A 1600 MET cc_start: 0.9168 (tpp) cc_final: 0.8762 (tpt) REVERT: A 1762 MET cc_start: 0.9527 (mmm) cc_final: 0.9265 (mmm) REVERT: A 1825 LEU cc_start: 0.9736 (tt) cc_final: 0.9462 (mt) REVERT: A 2274 ILE cc_start: 0.9784 (mm) cc_final: 0.9523 (tp) REVERT: A 2279 ILE cc_start: 0.8863 (mm) cc_final: 0.8661 (mm) REVERT: A 3111 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8707 (pmm) REVERT: A 3157 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9117 (mm) REVERT: A 3173 MET cc_start: 0.8699 (tpp) cc_final: 0.8167 (tpp) REVERT: A 3240 MET cc_start: 0.9219 (tpp) cc_final: 0.8984 (tpp) REVERT: A 3687 MET cc_start: 0.9356 (mtt) cc_final: 0.8841 (mtt) REVERT: A 3984 MET cc_start: 0.9195 (mtm) cc_final: 0.8944 (mtm) REVERT: B 38 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8205 (tt) REVERT: B 48 MET cc_start: 0.9195 (pmm) cc_final: 0.8393 (pmm) REVERT: B 161 MET cc_start: 0.8558 (mmm) cc_final: 0.8006 (mmm) REVERT: B 167 MET cc_start: 0.8085 (ppp) cc_final: 0.6773 (ppp) REVERT: B 346 MET cc_start: 0.9336 (tpt) cc_final: 0.9062 (tpp) REVERT: C 461 MET cc_start: 0.8221 (ppp) cc_final: 0.7926 (ppp) REVERT: C 515 MET cc_start: 0.9731 (ptp) cc_final: 0.9444 (ptp) outliers start: 33 outliers final: 18 residues processed: 176 average time/residue: 0.2177 time to fit residues: 67.3640 Evaluate side-chains 173 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1404 LYS Chi-restraints excluded: chain A residue 1743 MET Chi-restraints excluded: chain A residue 2221 LYS Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 3111 MET Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 236 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 190 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 420 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 366 optimal weight: 9.9990 chunk 188 optimal weight: 0.1980 chunk 416 optimal weight: 8.9990 chunk 151 optimal weight: 0.0970 chunk 330 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1304 HIS A2481 HIS ** A3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** 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 = 0.3206 r_free = 0.3206 target = 0.035449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.025961 restraints weight = 392622.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.026779 restraints weight = 229661.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.027328 restraints weight = 160309.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.027697 restraints weight = 125072.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.027964 restraints weight = 105444.064| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 39162 Z= 0.112 Angle : 0.622 11.243 53179 Z= 0.314 Chirality : 0.040 0.185 6063 Planarity : 0.004 0.053 6617 Dihedral : 12.147 84.536 5625 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.94 % Allowed : 15.35 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 4669 helix: 0.83 (0.11), residues: 2646 sheet: -0.64 (0.37), residues: 193 loop : -1.88 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 79 TYR 0.026 0.001 TYR A3610 PHE 0.024 0.001 PHE A2260 TRP 0.012 0.001 TRP A3916 HIS 0.003 0.001 HIS A1304 Details of bonding type rmsd covalent geometry : bond 0.00237 (39162) covalent geometry : angle 0.62212 (53179) hydrogen bonds : bond 0.03381 ( 1912) hydrogen bonds : angle 4.41378 ( 5585) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9544 (OUTLIER) cc_final: 0.9302 (pm20) REVERT: A 96 MET cc_start: 0.2466 (OUTLIER) cc_final: 0.0916 (mtm) REVERT: A 342 MET cc_start: 0.7561 (ppp) cc_final: 0.6913 (ppp) REVERT: A 366 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8737 (t80) REVERT: A 395 MET cc_start: 0.8961 (tpp) cc_final: 0.8720 (tpp) REVERT: A 540 MET cc_start: 0.9211 (mpp) cc_final: 0.8992 (mpp) REVERT: A 718 MET cc_start: 0.8903 (ppp) cc_final: 0.8663 (ppp) REVERT: A 754 MET cc_start: 0.9137 (tpp) cc_final: 0.8474 (tpp) REVERT: A 939 MET cc_start: 0.9214 (mmm) cc_final: 0.9010 (mmm) REVERT: A 1108 MET cc_start: 0.9327 (ttm) cc_final: 0.9050 (ttt) REVERT: A 1404 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9092 (mmtm) REVERT: A 1600 MET cc_start: 0.9106 (tpp) cc_final: 0.8735 (tpt) REVERT: A 1643 MET cc_start: 0.8984 (mpp) cc_final: 0.8759 (mpp) REVERT: A 1743 MET cc_start: 0.9578 (OUTLIER) cc_final: 0.8912 (mmt) REVERT: A 1762 MET cc_start: 0.9496 (mmm) cc_final: 0.9196 (mmm) REVERT: A 1825 LEU cc_start: 0.9694 (tt) cc_final: 0.9429 (mt) REVERT: A 2126 MET cc_start: 0.9204 (ppp) cc_final: 0.8955 (ppp) REVERT: A 2274 ILE cc_start: 0.9731 (mm) cc_final: 0.9450 (tp) REVERT: A 3111 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8608 (pmm) REVERT: A 3157 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9097 (mm) REVERT: A 3173 MET cc_start: 0.8468 (tpp) cc_final: 0.8022 (tpp) REVERT: A 3687 MET cc_start: 0.9306 (mtt) cc_final: 0.8662 (mtt) REVERT: A 3820 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8350 (ppp) REVERT: A 3984 MET cc_start: 0.9093 (mtm) cc_final: 0.8790 (mtm) REVERT: B 48 MET cc_start: 0.9141 (pmm) cc_final: 0.8352 (pmm) REVERT: B 161 MET cc_start: 0.8745 (mmm) cc_final: 0.8130 (mmm) REVERT: B 167 MET cc_start: 0.8085 (ppp) cc_final: 0.7156 (ppp) REVERT: B 346 MET cc_start: 0.9320 (tpt) cc_final: 0.9069 (tpp) REVERT: C 14 MET cc_start: 0.9201 (ppp) cc_final: 0.8934 (pmm) outliers start: 38 outliers final: 19 residues processed: 188 average time/residue: 0.2063 time to fit residues: 68.7379 Evaluate side-chains 176 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1404 LYS Chi-restraints excluded: chain A residue 1743 MET Chi-restraints excluded: chain A residue 1845 VAL Chi-restraints excluded: chain A residue 2221 LYS Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 3111 MET Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3820 MET Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 236 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 90 optimal weight: 0.0980 chunk 186 optimal weight: 9.9990 chunk 357 optimal weight: 7.9990 chunk 270 optimal weight: 0.9980 chunk 403 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 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 = 0.3207 r_free = 0.3207 target = 0.035485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.026022 restraints weight = 392003.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.026824 restraints weight = 230349.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.027386 restraints weight = 161049.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.027752 restraints weight = 125703.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.027998 restraints weight = 106040.382| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 39162 Z= 0.110 Angle : 0.618 11.956 53179 Z= 0.310 Chirality : 0.039 0.180 6063 Planarity : 0.004 0.053 6617 Dihedral : 12.063 85.274 5625 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.99 % Allowed : 15.62 % Favored : 83.39 % 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: -0.38 (0.13), residues: 4669 helix: 0.83 (0.11), residues: 2653 sheet: -0.56 (0.38), residues: 187 loop : -1.87 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.024 0.001 TYR A3610 PHE 0.021 0.001 PHE A2260 TRP 0.013 0.001 TRP A1633 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00240 (39162) covalent geometry : angle 0.61750 (53179) hydrogen bonds : bond 0.03323 ( 1912) hydrogen bonds : angle 4.36295 ( 5585) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9568 (OUTLIER) cc_final: 0.9284 (pm20) REVERT: A 96 MET cc_start: 0.2435 (OUTLIER) cc_final: 0.0915 (mtm) REVERT: A 333 MET cc_start: 0.8091 (ppp) cc_final: 0.7858 (ppp) REVERT: A 342 MET cc_start: 0.7627 (ppp) cc_final: 0.6979 (ppp) REVERT: A 395 MET cc_start: 0.9014 (tpp) cc_final: 0.8678 (tpp) REVERT: A 540 MET cc_start: 0.9250 (mpp) cc_final: 0.9023 (mpp) REVERT: A 718 MET cc_start: 0.8906 (ppp) cc_final: 0.8672 (ppp) REVERT: A 754 MET cc_start: 0.9163 (tpp) cc_final: 0.8488 (tpp) REVERT: A 1108 MET cc_start: 0.9312 (ttm) cc_final: 0.9033 (ttt) REVERT: A 1404 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9135 (mmtm) REVERT: A 1600 MET cc_start: 0.9094 (tpp) cc_final: 0.8773 (tpt) REVERT: A 1643 MET cc_start: 0.8984 (mpp) cc_final: 0.8729 (mpp) REVERT: A 1743 MET cc_start: 0.9572 (OUTLIER) cc_final: 0.8934 (mmt) REVERT: A 1757 MET cc_start: 0.9234 (tpt) cc_final: 0.9030 (tpp) REVERT: A 1825 LEU cc_start: 0.9699 (tt) cc_final: 0.9432 (mt) REVERT: A 2274 ILE cc_start: 0.9757 (mm) cc_final: 0.9494 (tp) REVERT: A 2473 MET cc_start: 0.9463 (ttp) cc_final: 0.9249 (ttp) REVERT: A 3111 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8625 (pmm) REVERT: A 3157 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9111 (mm) REVERT: A 3173 MET cc_start: 0.8503 (tpp) cc_final: 0.8039 (tpp) REVERT: A 3240 MET cc_start: 0.9153 (tpp) cc_final: 0.8859 (tpp) REVERT: A 3687 MET cc_start: 0.9316 (mtt) cc_final: 0.8665 (mtt) REVERT: A 3820 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8316 (ppp) REVERT: A 3984 MET cc_start: 0.9104 (mtm) cc_final: 0.8829 (mtm) REVERT: B 48 MET cc_start: 0.9171 (pmm) cc_final: 0.8383 (pmm) REVERT: B 167 MET cc_start: 0.8008 (ppp) cc_final: 0.7125 (ppp) REVERT: B 346 MET cc_start: 0.9297 (tpt) cc_final: 0.9034 (tpp) REVERT: C 14 MET cc_start: 0.9183 (ppp) cc_final: 0.8886 (pmm) REVERT: C 115 MET cc_start: 0.8873 (ppp) cc_final: 0.8662 (ppp) REVERT: C 495 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9446 (mm) outliers start: 40 outliers final: 20 residues processed: 186 average time/residue: 0.2164 time to fit residues: 71.4534 Evaluate side-chains 176 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1404 LYS Chi-restraints excluded: chain A residue 1743 MET Chi-restraints excluded: chain A residue 2221 LYS Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 3111 MET Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3820 MET Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 495 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 215 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 468 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 457 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 422 optimal weight: 6.9990 chunk 424 optimal weight: 20.0000 chunk 309 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3743 HIS ** A4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS C 162 GLN C 411 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.034301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.024888 restraints weight = 405482.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.025678 restraints weight = 237005.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.026215 restraints weight = 165765.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.026566 restraints weight = 129299.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.026828 restraints weight = 109111.140| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 39162 Z= 0.218 Angle : 0.691 10.529 53179 Z= 0.348 Chirality : 0.040 0.187 6063 Planarity : 0.004 0.052 6617 Dihedral : 12.098 89.399 5625 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.86 % Allowed : 15.99 % Favored : 83.14 % 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: -0.40 (0.13), residues: 4669 helix: 0.78 (0.10), residues: 2661 sheet: -0.55 (0.39), residues: 183 loop : -1.83 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.023 0.002 TYR A3610 PHE 0.019 0.002 PHE A2554 TRP 0.017 0.001 TRP A1633 HIS 0.008 0.001 HIS A2103 Details of bonding type rmsd covalent geometry : bond 0.00462 (39162) covalent geometry : angle 0.69078 (53179) hydrogen bonds : bond 0.03768 ( 1912) hydrogen bonds : angle 4.56721 ( 5585) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9587 (OUTLIER) cc_final: 0.9313 (pm20) REVERT: A 96 MET cc_start: 0.2795 (OUTLIER) cc_final: 0.1246 (mtm) REVERT: A 342 MET cc_start: 0.7643 (ppp) cc_final: 0.7013 (ppp) REVERT: A 366 TYR cc_start: 0.9317 (OUTLIER) cc_final: 0.8803 (t80) REVERT: A 395 MET cc_start: 0.9217 (tpp) cc_final: 0.8858 (tpp) REVERT: A 540 MET cc_start: 0.9324 (mpp) cc_final: 0.9061 (mpp) REVERT: A 718 MET cc_start: 0.9015 (ppp) cc_final: 0.8750 (ppp) REVERT: A 754 MET cc_start: 0.9186 (tpp) cc_final: 0.8551 (tpp) REVERT: A 879 MET cc_start: 0.8469 (mmm) cc_final: 0.7908 (mmm) REVERT: A 939 MET cc_start: 0.8875 (tpp) cc_final: 0.8198 (tpp) REVERT: A 1108 MET cc_start: 0.9362 (ttm) cc_final: 0.9082 (ttt) REVERT: A 1404 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9134 (mmtm) REVERT: A 1600 MET cc_start: 0.9079 (tpp) cc_final: 0.8762 (tpt) REVERT: A 1643 MET cc_start: 0.8971 (mpp) cc_final: 0.8727 (mpp) REVERT: A 1743 MET cc_start: 0.9618 (OUTLIER) cc_final: 0.8919 (mmt) REVERT: A 1825 LEU cc_start: 0.9715 (tt) cc_final: 0.9453 (mt) REVERT: A 2274 ILE cc_start: 0.9787 (mm) cc_final: 0.9572 (tp) REVERT: A 3111 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8697 (pmm) REVERT: A 3157 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9142 (mm) REVERT: A 3173 MET cc_start: 0.8714 (tpp) cc_final: 0.8253 (tpp) REVERT: A 3240 MET cc_start: 0.9173 (tpp) cc_final: 0.8889 (tpp) REVERT: A 3687 MET cc_start: 0.9376 (mtt) cc_final: 0.8770 (mtt) REVERT: A 3820 MET cc_start: 0.8616 (ppp) cc_final: 0.8361 (ppp) REVERT: A 3984 MET cc_start: 0.9140 (mtm) cc_final: 0.8893 (mtm) REVERT: B 48 MET cc_start: 0.9193 (pmm) cc_final: 0.8410 (pmm) REVERT: B 167 MET cc_start: 0.7928 (ppp) cc_final: 0.7133 (ppp) REVERT: C 389 MET cc_start: 0.7362 (mmm) cc_final: 0.7103 (mmm) outliers start: 35 outliers final: 23 residues processed: 179 average time/residue: 0.2134 time to fit residues: 67.5220 Evaluate side-chains 179 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1404 LYS Chi-restraints excluded: chain A residue 1743 MET Chi-restraints excluded: chain A residue 1845 VAL Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2221 LYS Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 3111 MET Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 40 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 325 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 341 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 334 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 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 = 0.3171 r_free = 0.3171 target = 0.034657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.025188 restraints weight = 400490.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.025975 restraints weight = 233901.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.026529 restraints weight = 163678.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.026889 restraints weight = 127607.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.027152 restraints weight = 107339.243| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39162 Z= 0.158 Angle : 0.662 11.717 53179 Z= 0.332 Chirality : 0.040 0.197 6063 Planarity : 0.004 0.052 6617 Dihedral : 12.088 89.780 5625 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.79 % Allowed : 16.14 % Favored : 83.07 % 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: -0.34 (0.13), residues: 4669 helix: 0.85 (0.10), residues: 2663 sheet: -0.72 (0.38), residues: 190 loop : -1.83 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1711 TYR 0.025 0.001 TYR A3610 PHE 0.019 0.001 PHE A2260 TRP 0.014 0.001 TRP A3916 HIS 0.006 0.001 HIS A2103 Details of bonding type rmsd covalent geometry : bond 0.00344 (39162) covalent geometry : angle 0.66170 (53179) hydrogen bonds : bond 0.03511 ( 1912) hydrogen bonds : angle 4.48656 ( 5585) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9338 Ramachandran restraints generated. 4669 Oldfield, 0 Emsley, 4669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9578 (OUTLIER) cc_final: 0.9303 (pm20) REVERT: A 96 MET cc_start: 0.2888 (OUTLIER) cc_final: 0.1325 (mtm) REVERT: A 342 MET cc_start: 0.7645 (ppp) cc_final: 0.7030 (ppp) REVERT: A 395 MET cc_start: 0.9190 (tpp) cc_final: 0.8915 (tpp) REVERT: A 540 MET cc_start: 0.9301 (mpp) cc_final: 0.9065 (mpp) REVERT: A 718 MET cc_start: 0.8998 (ppp) cc_final: 0.8750 (ppp) REVERT: A 754 MET cc_start: 0.9162 (tpp) cc_final: 0.8515 (tpp) REVERT: A 879 MET cc_start: 0.8429 (mmm) cc_final: 0.7855 (mmm) REVERT: A 939 MET cc_start: 0.8881 (tpp) cc_final: 0.8206 (tpp) REVERT: A 1108 MET cc_start: 0.9362 (ttm) cc_final: 0.9075 (ttt) REVERT: A 1404 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9162 (mmtm) REVERT: A 1600 MET cc_start: 0.9093 (tpp) cc_final: 0.8759 (tpt) REVERT: A 1643 MET cc_start: 0.8966 (mpp) cc_final: 0.8712 (mpp) REVERT: A 1743 MET cc_start: 0.9621 (OUTLIER) cc_final: 0.8931 (mmt) REVERT: A 1825 LEU cc_start: 0.9707 (tt) cc_final: 0.9446 (mt) REVERT: A 2274 ILE cc_start: 0.9775 (mm) cc_final: 0.9552 (tp) REVERT: A 3111 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8663 (pmm) REVERT: A 3157 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9153 (mm) REVERT: A 3173 MET cc_start: 0.8598 (tpp) cc_final: 0.8133 (tpp) REVERT: A 3240 MET cc_start: 0.9170 (tpp) cc_final: 0.8886 (tpp) REVERT: A 3687 MET cc_start: 0.9367 (mtt) cc_final: 0.8736 (mtt) REVERT: A 3820 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8457 (ppp) REVERT: A 3984 MET cc_start: 0.9110 (mtm) cc_final: 0.8840 (mtm) REVERT: B 48 MET cc_start: 0.9161 (pmm) cc_final: 0.8356 (pmm) REVERT: B 167 MET cc_start: 0.7969 (ppp) cc_final: 0.7172 (ppp) REVERT: C 14 MET cc_start: 0.9059 (pmm) cc_final: 0.8658 (pmm) REVERT: C 389 MET cc_start: 0.7488 (mmm) cc_final: 0.7195 (mmm) outliers start: 32 outliers final: 24 residues processed: 176 average time/residue: 0.2149 time to fit residues: 67.0634 Evaluate side-chains 179 residues out of total 4220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1404 LYS Chi-restraints excluded: chain A residue 1743 MET Chi-restraints excluded: chain A residue 1845 VAL Chi-restraints excluded: chain A residue 2221 LYS Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 3111 MET Chi-restraints excluded: chain A residue 3157 LEU Chi-restraints excluded: chain A residue 3182 ILE Chi-restraints excluded: chain A residue 3820 MET Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 227 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 402 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 393 optimal weight: 4.9990 chunk 444 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 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 = 0.3169 r_free = 0.3169 target = 0.034589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.025138 restraints weight = 401283.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.025932 restraints weight = 233552.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.026461 restraints weight = 163057.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.026841 restraints weight = 127946.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.027089 restraints weight = 107466.611| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39162 Z= 0.162 Angle : 0.667 17.084 53179 Z= 0.333 Chirality : 0.040 0.206 6063 Planarity : 0.004 0.051 6617 Dihedral : 12.075 87.632 5625 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.89 % Allowed : 16.14 % Favored : 82.97 % 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: -0.33 (0.13), residues: 4669 helix: 0.86 (0.10), residues: 2663 sheet: -0.69 (0.38), residues: 190 loop : -1.82 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.024 0.001 TYR A3610 PHE 0.019 0.001 PHE A2260 TRP 0.014 0.001 TRP A1633 HIS 0.005 0.001 HIS A3070 Details of bonding type rmsd covalent geometry : bond 0.00351 (39162) covalent geometry : angle 0.66711 (53179) hydrogen bonds : bond 0.03503 ( 1912) hydrogen bonds : angle 4.48927 ( 5585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6212.06 seconds wall clock time: 109 minutes 2.12 seconds (6542.12 seconds total)