Starting phenix.real_space_refine on Wed Mar 4 04:38:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x6v_33028/03_2026/7x6v_33028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x6v_33028/03_2026/7x6v_33028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x6v_33028/03_2026/7x6v_33028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x6v_33028/03_2026/7x6v_33028.map" model { file = "/net/cci-nas-00/data/ceres_data/7x6v_33028/03_2026/7x6v_33028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x6v_33028/03_2026/7x6v_33028.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 2 6.06 5 S 70 5.16 5 C 6941 2.51 5 N 1844 2.21 5 O 2045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s 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: 10903 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 360 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 43} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 10540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1381, 10537 Classifications: {'peptide': 1381} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 47, 'TRANS': 1333} Chain breaks: 13 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 819 Unresolved non-hydrogen dihedrals: 511 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'ARG:plan': 23, 'ASP:plan': 11, 'GLU:plan': 19, 'ASN:plan1': 6, 'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 294 Conformer: "B" Number of residues, atoms: 1381, 10537 Classifications: {'peptide': 1381} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 47, 'TRANS': 1333} Chain breaks: 13 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 819 Unresolved non-hydrogen dihedrals: 511 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'ARG:plan': 23, 'ASP:plan': 11, 'GLU:plan': 19, 'ASN:plan1': 6, 'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 294 bond proxies already assigned to first conformer: 10736 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36 SG CYS B 32 41.306 24.323 103.168 1.00 50.18 S ATOM 57 SG CYS B 35 37.933 24.447 101.079 1.00 49.75 S ATOM 188 SG CYS B 51 39.226 21.873 103.451 1.00 51.81 S ATOM 215 SG CYS B 54 39.869 22.028 100.449 1.00 49.13 S ATOM 140 SG CYS B 45 49.874 18.848 99.557 1.00 48.54 S ATOM 299 SG CYS B 65 47.958 18.767 96.163 1.00 54.85 S ATOM 320 SG CYS B 68 50.956 19.300 96.272 1.00 55.00 S Time building chain proxies: 4.23, per 1000 atoms: 0.39 Number of scatterers: 10903 At special positions: 0 Unit cell: (101.52, 112.32, 119.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Mn 1 24.99 S 70 16.00 O 2045 8.00 N 1844 7.00 C 6941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 775.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 51 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 35 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 32 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 54 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 65 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 45 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 68 " Number of angles added : 9 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2746 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 13 sheets defined 51.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'B' and resid 51 through 60 Processing helix chain 'A' and resid 2 through 16 removed outlier: 4.141A pdb=" N LEU A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.823A pdb=" N ARG A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 59 removed outlier: 3.625A pdb=" N ILE A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 76 removed outlier: 4.030A pdb=" N SER A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 126 removed outlier: 4.550A pdb=" N ILE A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 153 through 174 removed outlier: 3.541A pdb=" N ASN A 174 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.929A pdb=" N CYS A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.652A pdb=" N LEU A 249 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.609A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.751A pdb=" N LEU A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.553A pdb=" N GLU A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 442 through 447 removed outlier: 4.068A pdb=" N HIS A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 493 through 498 removed outlier: 3.595A pdb=" N THR A 498 " --> pdb=" O CYS A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 removed outlier: 3.710A pdb=" N LYS A 502 " --> pdb=" O ASN A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 573 through 577 removed outlier: 4.764A pdb=" N PHE A 577 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.801A pdb=" N ASP A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 592 No H-bonds generated for 'chain 'A' and resid 590 through 592' Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 602 through 620 removed outlier: 3.559A pdb=" N LEU A 616 " --> pdb=" O THR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 640 removed outlier: 3.741A pdb=" N VAL A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N TYR A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 636 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.614A pdb=" N ASP A 650 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 676 removed outlier: 4.202A pdb=" N TYR A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 697 removed outlier: 3.787A pdb=" N LYS A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 701 removed outlier: 3.738A pdb=" N ILE A 701 " --> pdb=" O CYS A 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 698 through 701' Processing helix chain 'A' and resid 708 through 727 removed outlier: 4.396A pdb=" N LYS A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 3.669A pdb=" N GLN A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 752 removed outlier: 3.694A pdb=" N THR A 752 " --> pdb=" O MET A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 779 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 866 through 872 removed outlier: 4.368A pdb=" N VAL A 869 " --> pdb=" O SER A 866 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 870 " --> pdb=" O ARG A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.595A pdb=" N LEU A1088 " --> pdb=" O LEU A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1148 removed outlier: 3.907A pdb=" N ARG A1137 " --> pdb=" O LYS A1133 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A1138 " --> pdb=" O MET A1134 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A1139 " --> pdb=" O PHE A1135 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A1144 " --> pdb=" O GLU A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1173 removed outlier: 3.737A pdb=" N PHE A1161 " --> pdb=" O ASN A1157 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A1162 " --> pdb=" O ASP A1158 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1200 removed outlier: 3.653A pdb=" N PHE A1195 " --> pdb=" O CYS A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1226 removed outlier: 4.435A pdb=" N THR A1219 " --> pdb=" O ASP A1215 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP A1223 " --> pdb=" O THR A1219 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS A1226 " --> pdb=" O THR A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1249 Processing helix chain 'A' and resid 1258 through 1270 removed outlier: 3.527A pdb=" N ILE A1262 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG A1264 " --> pdb=" O GLU A1260 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A1270 " --> pdb=" O TYR A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1311 removed outlier: 3.612A pdb=" N ASN A1303 " --> pdb=" O GLU A1299 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A1304 " --> pdb=" O ARG A1300 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A1307 " --> pdb=" O ASN A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1338 removed outlier: 3.793A pdb=" N LEU A1334 " --> pdb=" O ARG A1330 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL A1335 " --> pdb=" O LEU A1331 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A1336 " --> pdb=" O SER A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1356 removed outlier: 3.819A pdb=" N SER A1350 " --> pdb=" O LEU A1346 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A1353 " --> pdb=" O GLN A1349 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1395 removed outlier: 3.616A pdb=" N PHE A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A1392 " --> pdb=" O THR A1388 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A1393 " --> pdb=" O LYS A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1420 removed outlier: 4.284A pdb=" N GLU A1408 " --> pdb=" O HIS A1404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A1410 " --> pdb=" O LEU A1406 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A1411 " --> pdb=" O CYS A1407 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP A1415 " --> pdb=" O ASP A1411 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A1420 " --> pdb=" O GLN A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1441 removed outlier: 3.919A pdb=" N SER A1429 " --> pdb=" O SER A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1476 removed outlier: 3.735A pdb=" N ARG A1467 " --> pdb=" O SER A1463 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A1468 " --> pdb=" O ARG A1464 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A1474 " --> pdb=" O ARG A1470 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS A1476 " --> pdb=" O ILE A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.515A pdb=" N LYS A1481 " --> pdb=" O ASN A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1493 Processing helix chain 'A' and resid 1501 through 1508 Processing helix chain 'A' and resid 1514 through 1524 removed outlier: 3.822A pdb=" N LEU A1523 " --> pdb=" O LEU A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1534 removed outlier: 4.398A pdb=" N LEU A1532 " --> pdb=" O ASP A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1576 Processing helix chain 'A' and resid 1606 through 1614 removed outlier: 4.484A pdb=" N LYS A1612 " --> pdb=" O ILE A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1639 removed outlier: 3.796A pdb=" N LEU A1632 " --> pdb=" O TYR A1628 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP A1635 " --> pdb=" O LYS A1631 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A1636 " --> pdb=" O LEU A1632 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR A1637 " --> pdb=" O LEU A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1660 Processing helix chain 'A' and resid 1675 through 1690 removed outlier: 3.906A pdb=" N ILE A1680 " --> pdb=" O LEU A1676 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1682 " --> pdb=" O ASP A1678 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER A1687 " --> pdb=" O SER A1683 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A1689 " --> pdb=" O SER A1685 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A1690 " --> pdb=" O ASN A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1696 Processing helix chain 'A' and resid 1733 through 1743 Processing helix chain 'A' and resid 1747 through 1752 Processing helix chain 'A' and resid 1774 through 1785 removed outlier: 3.582A pdb=" N SER A1785 " --> pdb=" O ILE A1781 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.804A pdb=" N TYR B 70 " --> pdb=" O CYS B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.425A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA6, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA7, first strand: chain 'A' and resid 551 through 553 removed outlier: 3.956A pdb=" N ARG A 551 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 567 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 565 " --> pdb=" O TYR A 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1113 through 1115 Processing sheet with id=AA9, first strand: chain 'A' and resid 1183 through 1184 removed outlier: 4.587A pdb=" N PHE A1359 " --> pdb=" O SER A1184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1229 through 1230 Processing sheet with id=AB2, first strand: chain 'A' and resid 1315 through 1316 removed outlier: 4.148A pdb=" N GLU A1315 " --> pdb=" O LEU A1326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1536 through 1538 Processing sheet with id=AB4, first strand: chain 'A' and resid 1619 through 1620 removed outlier: 3.807A pdb=" N VAL A1619 " --> pdb=" O LEU A1627 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.22: 57 1.22 - 1.37: 3966 1.37 - 1.52: 4055 1.52 - 1.66: 2937 1.66 - 1.81: 99 Bond restraints: 11114 Sorted by residual: bond pdb=" C ALA A1371 " pdb=" O ALA A1371 " ideal model delta sigma weight residual 1.234 1.078 0.155 1.20e-02 6.94e+03 1.68e+02 bond pdb=" C HIS B 53 " pdb=" N CYS B 54 " ideal model delta sigma weight residual 1.332 1.500 -0.167 1.40e-02 5.10e+03 1.43e+02 bond pdb=" C CYS B 54 " pdb=" N LEU B 55 " ideal model delta sigma weight residual 1.334 1.498 -0.163 1.43e-02 4.89e+03 1.30e+02 bond pdb=" C ASP A1182 " pdb=" O ASP A1182 " ideal model delta sigma weight residual 1.235 1.106 0.129 1.26e-02 6.30e+03 1.05e+02 bond pdb=" C ASP A1322 " pdb=" O ASP A1322 " ideal model delta sigma weight residual 1.234 1.133 0.101 1.07e-02 8.73e+03 8.87e+01 ... (remaining 11109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.01: 14942 8.01 - 16.01: 93 16.01 - 24.02: 7 24.02 - 32.02: 1 32.02 - 40.03: 1 Bond angle restraints: 15044 Sorted by residual: angle pdb=" O HIS B 53 " pdb=" C HIS B 53 " pdb=" N CYS B 54 " ideal model delta sigma weight residual 122.59 82.56 40.03 1.33e+00 5.65e-01 9.06e+02 angle pdb=" N ASP B 40 " pdb=" CA ASP B 40 " pdb=" C ASP B 40 " ideal model delta sigma weight residual 113.02 140.87 -27.85 1.49e+00 4.50e-01 3.49e+02 angle pdb=" N PHE A1369 " pdb=" CA PHE A1369 " pdb=" C PHE A1369 " ideal model delta sigma weight residual 113.89 133.24 -19.35 1.58e+00 4.01e-01 1.50e+02 angle pdb=" O SER A1787 " pdb=" C SER A1787 " pdb=" N LEU A1788 " ideal model delta sigma weight residual 122.10 138.39 -16.29 1.34e+00 5.57e-01 1.48e+02 angle pdb=" N ASN A 473 " pdb=" CA ASN A 473 " pdb=" C ASN A 473 " ideal model delta sigma weight residual 109.76 90.03 19.73 1.64e+00 3.72e-01 1.45e+02 ... (remaining 15039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5972 18.00 - 36.01: 617 36.01 - 54.01: 97 54.01 - 72.01: 17 72.01 - 90.02: 7 Dihedral angle restraints: 6710 sinusoidal: 2506 harmonic: 4204 Sorted by residual: dihedral pdb=" C ILE A 484 " pdb=" N ILE A 484 " pdb=" CA ILE A 484 " pdb=" CB ILE A 484 " ideal model delta harmonic sigma weight residual -122.00 -151.70 29.70 0 2.50e+00 1.60e-01 1.41e+02 dihedral pdb=" C THR A1480 " pdb=" N THR A1480 " pdb=" CA THR A1480 " pdb=" CB THR A1480 " ideal model delta harmonic sigma weight residual -122.00 -149.18 27.18 0 2.50e+00 1.60e-01 1.18e+02 dihedral pdb=" N ASP B 40 " pdb=" C ASP B 40 " pdb=" CA ASP B 40 " pdb=" CB ASP B 40 " ideal model delta harmonic sigma weight residual 122.80 148.90 -26.10 0 2.50e+00 1.60e-01 1.09e+02 ... (remaining 6707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 1661 0.286 - 0.572: 34 0.572 - 0.857: 10 0.857 - 1.143: 4 1.143 - 1.429: 2 Chirality restraints: 1711 Sorted by residual: chirality pdb=" CA ASP B 40 " pdb=" N ASP B 40 " pdb=" C ASP B 40 " pdb=" CB ASP B 40 " both_signs ideal model delta sigma weight residual False 2.51 1.08 1.43 2.00e-01 2.50e+01 5.11e+01 chirality pdb=" CA ILE A 484 " pdb=" N ILE A 484 " pdb=" C ILE A 484 " pdb=" CB ILE A 484 " both_signs ideal model delta sigma weight residual False 2.43 1.27 1.16 2.00e-01 2.50e+01 3.37e+01 chirality pdb=" CA THR A1480 " pdb=" N THR A1480 " pdb=" C THR A1480 " pdb=" CB THR A1480 " both_signs ideal model delta sigma weight residual False 2.53 1.39 1.13 2.00e-01 2.50e+01 3.21e+01 ... (remaining 1708 not shown) Planarity restraints: 1943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 53 " -0.149 2.00e-02 2.50e+03 2.28e-01 5.19e+02 pdb=" C HIS B 53 " 0.392 2.00e-02 2.50e+03 pdb=" O HIS B 53 " -0.153 2.00e-02 2.50e+03 pdb=" N CYS B 54 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1497 " -0.038 2.00e-02 2.50e+03 7.50e-02 5.63e+01 pdb=" C GLY A1497 " 0.130 2.00e-02 2.50e+03 pdb=" O GLY A1497 " -0.048 2.00e-02 2.50e+03 pdb=" N GLU A1498 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 478 " -0.036 2.00e-02 2.50e+03 7.37e-02 5.43e+01 pdb=" C THR A 478 " 0.127 2.00e-02 2.50e+03 pdb=" O THR A 478 " -0.048 2.00e-02 2.50e+03 pdb=" N GLU A 479 " -0.043 2.00e-02 2.50e+03 ... (remaining 1940 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 24 2.29 - 2.94: 5478 2.94 - 3.60: 15131 3.60 - 4.25: 22350 4.25 - 4.90: 37047 Nonbonded interactions: 80030 Sorted by model distance: nonbonded pdb=" O LEU A1334 " pdb=" O ASP A1338 " model vdw 1.640 3.040 nonbonded pdb=" OD1 ASP A1182 " pdb="MN MN A2301 " model vdw 1.955 2.320 nonbonded pdb=" OE1 GLU A1372 " pdb="MN MN A2301 " model vdw 1.956 2.320 nonbonded pdb=" OE2 GLU A1372 " pdb="MN MN A2301 " model vdw 1.966 2.320 nonbonded pdb=" OD1 ASN A 499 " pdb=" OH TYR A 543 " model vdw 1.966 3.040 ... (remaining 80025 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=0.11 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.170 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 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 : 0.012 0.612 11123 Z= 0.594 Angle : 1.577 40.026 15053 Z= 0.903 Chirality : 0.116 1.429 1711 Planarity : 0.009 0.228 1943 Dihedral : 14.934 90.016 3964 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 1.00 % Allowed : 14.65 % Favored : 84.35 % Rotamer: Outliers : 0.62 % Allowed : 0.80 % Favored : 98.58 % Cbeta Deviations : 2.48 % 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: -3.94 (0.20), residues: 1400 helix: -1.53 (0.19), residues: 681 sheet: -2.69 (0.58), residues: 79 loop : -3.92 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 611 TYR 0.022 0.003 TYR A1803 PHE 0.042 0.003 PHE A 299 TRP 0.017 0.003 TRP B 36 HIS 0.009 0.002 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.01065 (11114) covalent geometry : angle 1.51597 (15044) hydrogen bonds : bond 0.17195 ( 408) hydrogen bonds : angle 7.43674 ( 1167) metal coordination : bond 0.22240 ( 8) metal coordination : angle 17.81842 ( 9) Misc. bond : bond 0.01997 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 199 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 MET cc_start: 0.8722 (mmm) cc_final: 0.8456 (tpt) REVERT: A 1654 TYR cc_start: 0.5580 (m-80) cc_final: 0.2677 (m-80) REVERT: A 1775 LEU cc_start: 0.8765 (tp) cc_final: 0.8555 (tp) REVERT: A 1807 PHE cc_start: 0.7801 (t80) cc_final: 0.7207 (m-80) outliers start: 7 outliers final: 3 residues processed: 206 average time/residue: 0.1003 time to fit residues: 29.2981 Evaluate side-chains 132 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain A residue 1372 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN A1087 ASN A1208 GLN A1492 HIS ** A1575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.198546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153304 restraints weight = 19186.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.152239 restraints weight = 11808.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.154436 restraints weight = 8549.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.154884 restraints weight = 6085.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.155369 restraints weight = 5505.852| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4071 r_free = 0.4071 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4071 r_free = 0.4071 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11123 Z= 0.192 Angle : 0.842 14.816 15053 Z= 0.425 Chirality : 0.047 0.287 1711 Planarity : 0.006 0.074 1943 Dihedral : 6.613 44.514 1517 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.87 % Favored : 87.99 % Rotamer: Outliers : 1.24 % Allowed : 9.68 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.38 (0.21), residues: 1400 helix: -1.08 (0.19), residues: 687 sheet: -2.07 (0.69), residues: 65 loop : -3.68 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1330 TYR 0.019 0.002 TYR A 745 PHE 0.035 0.002 PHE A1390 TRP 0.014 0.002 TRP A1223 HIS 0.012 0.001 HIS A1492 Details of bonding type rmsd covalent geometry : bond 0.00397 (11114) covalent geometry : angle 0.82478 (15044) hydrogen bonds : bond 0.04311 ( 408) hydrogen bonds : angle 5.30164 ( 1167) metal coordination : bond 0.02059 ( 8) metal coordination : angle 6.98243 ( 9) Misc. bond : bond 0.00184 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8166 (pt) cc_final: 0.7891 (pt) REVERT: A 323 MET cc_start: 0.6282 (tpp) cc_final: 0.5776 (mpp) REVERT: A 585 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7457 (ttm) REVERT: A 1498 GLU cc_start: 0.6401 (tp30) cc_final: 0.5692 (mp0) REVERT: A 1654 TYR cc_start: 0.5313 (m-80) cc_final: 0.2820 (m-80) REVERT: A 1807 PHE cc_start: 0.8242 (t80) cc_final: 0.7965 (t80) outliers start: 14 outliers final: 8 residues processed: 146 average time/residue: 0.0869 time to fit residues: 18.9911 Evaluate side-chains 130 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1412 THR Chi-restraints excluded: chain A residue 1777 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 122 optimal weight: 7.9990 chunk 85 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN A1492 HIS ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.199739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.152482 restraints weight = 16101.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.151684 restraints weight = 10242.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.154062 restraints weight = 8154.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.156526 restraints weight = 5864.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.156423 restraints weight = 5383.575| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4102 r_free = 0.4102 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4102 r_free = 0.4102 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11123 Z= 0.127 Angle : 0.725 12.859 15053 Z= 0.367 Chirality : 0.043 0.199 1711 Planarity : 0.005 0.070 1943 Dihedral : 5.900 32.482 1512 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.36 % Favored : 89.49 % Rotamer: Outliers : 1.42 % Allowed : 11.63 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.94 (0.21), residues: 1400 helix: -0.73 (0.20), residues: 682 sheet: -1.25 (0.66), residues: 66 loop : -3.50 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 185 TYR 0.015 0.001 TYR A 745 PHE 0.021 0.002 PHE A 388 TRP 0.009 0.001 TRP A1223 HIS 0.013 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00268 (11114) covalent geometry : angle 0.71051 (15044) hydrogen bonds : bond 0.03800 ( 408) hydrogen bonds : angle 4.90353 ( 1167) metal coordination : bond 0.00408 ( 8) metal coordination : angle 6.00085 ( 9) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.6600 (mpt180) cc_final: 0.5213 (mtm180) REVERT: A 205 ILE cc_start: 0.8191 (pt) cc_final: 0.7909 (pt) REVERT: A 1134 MET cc_start: 0.8037 (tpp) cc_final: 0.7623 (tpp) REVERT: A 1498 GLU cc_start: 0.6055 (tp30) cc_final: 0.5484 (mp0) outliers start: 16 outliers final: 7 residues processed: 138 average time/residue: 0.0862 time to fit residues: 18.1044 Evaluate side-chains 126 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1791 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 130 optimal weight: 0.0870 chunk 127 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS A1208 GLN A1492 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.183938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.128933 restraints weight = 26417.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129636 restraints weight = 15715.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132790 restraints weight = 9844.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133644 restraints weight = 7146.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134392 restraints weight = 6561.036| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11123 Z= 0.230 Angle : 0.828 18.972 15053 Z= 0.414 Chirality : 0.047 0.274 1711 Planarity : 0.005 0.074 1943 Dihedral : 6.225 31.485 1512 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.72 % Favored : 86.13 % Rotamer: Outliers : 2.49 % Allowed : 13.32 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.98 (0.22), residues: 1400 helix: -0.84 (0.19), residues: 691 sheet: -2.11 (0.62), residues: 79 loop : -3.34 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 185 TYR 0.027 0.002 TYR A 543 PHE 0.060 0.003 PHE A 720 TRP 0.009 0.002 TRP A1186 HIS 0.011 0.002 HIS A1492 Details of bonding type rmsd covalent geometry : bond 0.00531 (11114) covalent geometry : angle 0.80344 (15044) hydrogen bonds : bond 0.04378 ( 408) hydrogen bonds : angle 5.13381 ( 1167) metal coordination : bond 0.01080 ( 8) metal coordination : angle 8.23411 ( 9) Misc. bond : bond 0.00125 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.442 Fit side-chains REVERT: A 205 ILE cc_start: 0.8605 (pt) cc_final: 0.8322 (pt) REVERT: A 323 MET cc_start: 0.6430 (tpp) cc_final: 0.6035 (tpp) REVERT: A 464 MET cc_start: 0.5952 (OUTLIER) cc_final: 0.5295 (ppp) REVERT: A 770 PHE cc_start: 0.8866 (t80) cc_final: 0.8632 (t80) REVERT: A 1134 MET cc_start: 0.8202 (tpp) cc_final: 0.7595 (tpp) REVERT: A 1328 ASP cc_start: 0.7274 (t0) cc_final: 0.6968 (t0) REVERT: A 1338 ASP cc_start: 0.7253 (t70) cc_final: 0.7017 (t0) REVERT: A 1498 GLU cc_start: 0.6632 (tp30) cc_final: 0.6070 (mp0) REVERT: A 1808 SER cc_start: 0.8264 (t) cc_final: 0.7881 (t) outliers start: 28 outliers final: 14 residues processed: 139 average time/residue: 0.0786 time to fit residues: 17.0449 Evaluate side-chains 118 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1412 THR Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1791 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 23 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 0.0670 chunk 37 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 561 HIS A1208 GLN A1492 HIS ** A1661 HIS ** 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 = 0.4510 r_free = 0.4510 target = 0.195999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.144155 restraints weight = 15627.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.142196 restraints weight = 9512.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.145115 restraints weight = 7759.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.145731 restraints weight = 5706.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.146127 restraints weight = 5281.626| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3977 r_free = 0.3977 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11123 Z= 0.125 Angle : 0.708 14.791 15053 Z= 0.353 Chirality : 0.043 0.200 1711 Planarity : 0.004 0.070 1943 Dihedral : 5.707 30.247 1512 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.01 % Favored : 89.85 % Rotamer: Outliers : 1.07 % Allowed : 16.16 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.63 (0.22), residues: 1400 helix: -0.50 (0.20), residues: 693 sheet: -1.84 (0.62), residues: 76 loop : -3.26 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.025 0.001 TYR A1179 PHE 0.028 0.002 PHE A 720 TRP 0.007 0.001 TRP A1537 HIS 0.021 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00276 (11114) covalent geometry : angle 0.68956 (15044) hydrogen bonds : bond 0.03552 ( 408) hydrogen bonds : angle 4.76598 ( 1167) metal coordination : bond 0.00437 ( 8) metal coordination : angle 6.56990 ( 9) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.365 Fit side-chains REVERT: A 205 ILE cc_start: 0.8703 (pt) cc_final: 0.8499 (pt) REVERT: A 323 MET cc_start: 0.6447 (tpp) cc_final: 0.5995 (tpp) REVERT: A 770 PHE cc_start: 0.8788 (t80) cc_final: 0.8488 (t80) REVERT: A 1134 MET cc_start: 0.8076 (tpp) cc_final: 0.7777 (tpp) REVERT: A 1328 ASP cc_start: 0.7151 (t0) cc_final: 0.6832 (t70) REVERT: A 1332 SER cc_start: 0.9180 (t) cc_final: 0.8458 (p) REVERT: A 1498 GLU cc_start: 0.6464 (tp30) cc_final: 0.6027 (mp0) outliers start: 12 outliers final: 8 residues processed: 120 average time/residue: 0.0835 time to fit residues: 15.4445 Evaluate side-chains 109 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1788 LEU Chi-restraints excluded: chain A residue 1791 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 561 HIS A1208 GLN A1492 HIS ** A1661 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 = 0.4455 r_free = 0.4455 target = 0.190323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.139290 restraints weight = 31371.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.137872 restraints weight = 14922.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139929 restraints weight = 12252.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.140837 restraints weight = 8109.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.142273 restraints weight = 7400.683| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11123 Z= 0.175 Angle : 0.734 14.573 15053 Z= 0.369 Chirality : 0.045 0.201 1711 Planarity : 0.005 0.073 1943 Dihedral : 5.727 29.621 1512 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.79 % Favored : 87.06 % Rotamer: Outliers : 1.60 % Allowed : 16.87 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.22), residues: 1400 helix: -0.40 (0.20), residues: 686 sheet: -2.01 (0.62), residues: 80 loop : -3.17 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 395 TYR 0.018 0.002 TYR A 274 PHE 0.024 0.002 PHE A 299 TRP 0.008 0.001 TRP A1186 HIS 0.011 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00405 (11114) covalent geometry : angle 0.71739 (15044) hydrogen bonds : bond 0.03794 ( 408) hydrogen bonds : angle 4.81837 ( 1167) metal coordination : bond 0.00564 ( 8) metal coordination : angle 6.47772 ( 9) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.433 Fit side-chains REVERT: A 205 ILE cc_start: 0.8787 (pt) cc_final: 0.8537 (pt) REVERT: A 323 MET cc_start: 0.6765 (tpp) cc_final: 0.6310 (tpp) REVERT: A 464 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5667 (ppp) REVERT: A 745 TYR cc_start: 0.7434 (m-80) cc_final: 0.7220 (m-80) REVERT: A 1134 MET cc_start: 0.7985 (tpp) cc_final: 0.7655 (tpp) REVERT: A 1332 SER cc_start: 0.9157 (t) cc_final: 0.8457 (p) REVERT: A 1498 GLU cc_start: 0.6885 (tp30) cc_final: 0.6265 (mp0) REVERT: A 1808 SER cc_start: 0.8250 (t) cc_final: 0.7857 (t) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 0.0825 time to fit residues: 15.4003 Evaluate side-chains 116 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1412 THR Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1791 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS A1208 GLN A1492 HIS ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.171217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117270 restraints weight = 17245.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121632 restraints weight = 8688.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124580 restraints weight = 5722.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126450 restraints weight = 4431.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.127363 restraints weight = 3795.011| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11123 Z= 0.134 Angle : 0.700 13.325 15053 Z= 0.350 Chirality : 0.043 0.200 1711 Planarity : 0.004 0.071 1943 Dihedral : 5.539 29.675 1512 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.22 % Favored : 88.63 % Rotamer: Outliers : 1.24 % Allowed : 18.03 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.22), residues: 1400 helix: -0.29 (0.20), residues: 692 sheet: -1.90 (0.61), residues: 80 loop : -3.07 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 395 TYR 0.017 0.001 TYR A 745 PHE 0.019 0.001 PHE A1508 TRP 0.006 0.001 TRP A1537 HIS 0.023 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00306 (11114) covalent geometry : angle 0.68475 (15044) hydrogen bonds : bond 0.03405 ( 408) hydrogen bonds : angle 4.60847 ( 1167) metal coordination : bond 0.00527 ( 8) metal coordination : angle 5.92791 ( 9) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.379 Fit side-chains REVERT: A 163 LEU cc_start: 0.8061 (mt) cc_final: 0.7659 (pp) REVERT: A 205 ILE cc_start: 0.8868 (pt) cc_final: 0.8600 (pt) REVERT: A 323 MET cc_start: 0.6922 (tpp) cc_final: 0.6464 (tpp) REVERT: A 464 MET cc_start: 0.5666 (OUTLIER) cc_final: 0.5428 (ppp) REVERT: A 1134 MET cc_start: 0.8010 (tpp) cc_final: 0.7631 (tpp) REVERT: A 1332 SER cc_start: 0.9123 (t) cc_final: 0.8369 (p) REVERT: A 1498 GLU cc_start: 0.6555 (tp30) cc_final: 0.6294 (mp0) outliers start: 14 outliers final: 12 residues processed: 110 average time/residue: 0.0849 time to fit residues: 14.4564 Evaluate side-chains 113 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1788 LEU Chi-restraints excluded: chain A residue 1791 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 6 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 141 optimal weight: 0.0470 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS A1492 HIS ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.172522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119719 restraints weight = 14882.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123907 restraints weight = 7918.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126630 restraints weight = 5379.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128210 restraints weight = 4256.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128939 restraints weight = 3717.931| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11123 Z= 0.113 Angle : 0.671 12.534 15053 Z= 0.335 Chirality : 0.042 0.199 1711 Planarity : 0.004 0.071 1943 Dihedral : 5.281 29.643 1512 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.44 % Favored : 89.42 % Rotamer: Outliers : 1.33 % Allowed : 18.12 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.22), residues: 1400 helix: -0.04 (0.20), residues: 692 sheet: -1.84 (0.59), residues: 82 loop : -3.03 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 395 TYR 0.013 0.001 TYR A 543 PHE 0.020 0.001 PHE A 112 TRP 0.007 0.001 TRP A1537 HIS 0.032 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00249 (11114) covalent geometry : angle 0.65714 (15044) hydrogen bonds : bond 0.03114 ( 408) hydrogen bonds : angle 4.42906 ( 1167) metal coordination : bond 0.00535 ( 8) metal coordination : angle 5.57798 ( 9) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.6862 (tpp) cc_final: 0.6421 (tpp) REVERT: A 464 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.5496 (ppp) REVERT: A 745 TYR cc_start: 0.7325 (m-10) cc_final: 0.6831 (m-10) REVERT: A 1134 MET cc_start: 0.8006 (tpp) cc_final: 0.7524 (tpp) REVERT: A 1332 SER cc_start: 0.9052 (t) cc_final: 0.8292 (p) REVERT: A 1452 THR cc_start: 0.8514 (m) cc_final: 0.8240 (m) REVERT: A 1498 GLU cc_start: 0.6570 (tp30) cc_final: 0.6188 (mp0) outliers start: 15 outliers final: 11 residues processed: 117 average time/residue: 0.0830 time to fit residues: 14.9936 Evaluate side-chains 105 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1788 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 88 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 49 optimal weight: 0.4980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS A1208 GLN A1492 HIS ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.171128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116120 restraints weight = 17805.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120724 restraints weight = 8699.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123636 restraints weight = 5629.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125647 restraints weight = 4338.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126786 restraints weight = 3710.244| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11123 Z= 0.129 Angle : 0.678 13.160 15053 Z= 0.338 Chirality : 0.042 0.193 1711 Planarity : 0.004 0.071 1943 Dihedral : 5.189 29.447 1512 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.51 % Favored : 89.28 % Rotamer: Outliers : 1.15 % Allowed : 18.47 % Favored : 80.37 % 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: -1.97 (0.23), residues: 1400 helix: 0.08 (0.20), residues: 691 sheet: -1.79 (0.59), residues: 82 loop : -2.95 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 395 TYR 0.014 0.001 TYR A 566 PHE 0.018 0.001 PHE A1508 TRP 0.006 0.001 TRP A1223 HIS 0.017 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00295 (11114) covalent geometry : angle 0.66416 (15044) hydrogen bonds : bond 0.03193 ( 408) hydrogen bonds : angle 4.39463 ( 1167) metal coordination : bond 0.00520 ( 8) metal coordination : angle 5.70691 ( 9) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.448 Fit side-chains REVERT: A 323 MET cc_start: 0.7046 (tpp) cc_final: 0.6597 (tpp) REVERT: A 1134 MET cc_start: 0.7924 (tpp) cc_final: 0.7440 (tpp) REVERT: A 1328 ASP cc_start: 0.7094 (t0) cc_final: 0.6671 (t0) REVERT: A 1332 SER cc_start: 0.8926 (t) cc_final: 0.8174 (p) REVERT: A 1452 THR cc_start: 0.8566 (m) cc_final: 0.8306 (m) REVERT: A 1498 GLU cc_start: 0.6522 (tp30) cc_final: 0.6292 (mp0) outliers start: 13 outliers final: 10 residues processed: 110 average time/residue: 0.0799 time to fit residues: 13.6903 Evaluate side-chains 108 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1788 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 30.0000 chunk 100 optimal weight: 0.0030 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 0.0040 chunk 77 optimal weight: 0.0770 chunk 90 optimal weight: 0.0770 chunk 136 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 36 optimal weight: 0.0370 overall best weight: 0.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 561 HIS A1122 ASN A1492 HIS A1500 ASN ** A1661 HIS ** 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 = 0.4186 r_free = 0.4186 target = 0.175009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127805 restraints weight = 17764.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127327 restraints weight = 10596.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128993 restraints weight = 8478.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.129485 restraints weight = 5877.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.129909 restraints weight = 5315.382| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11123 Z= 0.114 Angle : 0.676 11.607 15053 Z= 0.335 Chirality : 0.042 0.250 1711 Planarity : 0.004 0.070 1943 Dihedral : 4.989 29.455 1512 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.22 % Favored : 90.56 % Rotamer: Outliers : 0.53 % Allowed : 19.09 % Favored : 80.37 % 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: -1.73 (0.23), residues: 1400 helix: 0.32 (0.21), residues: 693 sheet: -1.80 (0.61), residues: 73 loop : -2.86 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 395 TYR 0.025 0.001 TYR A 183 PHE 0.023 0.001 PHE A 112 TRP 0.007 0.001 TRP A1537 HIS 0.012 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00245 (11114) covalent geometry : angle 0.66432 (15044) hydrogen bonds : bond 0.02897 ( 408) hydrogen bonds : angle 4.24402 ( 1167) metal coordination : bond 0.00534 ( 8) metal coordination : angle 5.13040 ( 9) Misc. bond : bond 0.00004 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 104 PHE cc_start: 0.7617 (p90) cc_final: 0.7293 (p90) REVERT: A 286 LEU cc_start: 0.8878 (tp) cc_final: 0.8551 (mp) REVERT: A 323 MET cc_start: 0.7042 (tpp) cc_final: 0.6599 (tpp) REVERT: A 434 HIS cc_start: 0.5487 (t-90) cc_final: 0.5232 (t-90) REVERT: A 1134 MET cc_start: 0.7750 (tpp) cc_final: 0.7286 (tpp) REVERT: A 1328 ASP cc_start: 0.7009 (t0) cc_final: 0.6709 (t0) REVERT: A 1332 SER cc_start: 0.8906 (t) cc_final: 0.8171 (p) REVERT: A 1498 GLU cc_start: 0.6690 (tp30) cc_final: 0.6101 (mp0) outliers start: 6 outliers final: 4 residues processed: 110 average time/residue: 0.0846 time to fit residues: 14.2814 Evaluate side-chains 104 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 37 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 101 optimal weight: 0.0040 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN A1492 HIS ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.174967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121854 restraints weight = 23400.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125887 restraints weight = 11118.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128977 restraints weight = 6338.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129824 restraints weight = 4608.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130485 restraints weight = 4328.505| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11123 Z= 0.115 Angle : 0.669 12.104 15053 Z= 0.330 Chirality : 0.042 0.192 1711 Planarity : 0.004 0.071 1943 Dihedral : 4.940 29.342 1512 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.65 % Favored : 90.14 % Rotamer: Outliers : 0.71 % Allowed : 18.83 % Favored : 80.46 % 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: -1.68 (0.23), residues: 1400 helix: 0.45 (0.21), residues: 686 sheet: -2.25 (0.56), residues: 84 loop : -2.84 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 395 TYR 0.020 0.001 TYR A 745 PHE 0.017 0.001 PHE A1508 TRP 0.006 0.001 TRP A1223 HIS 0.020 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00260 (11114) covalent geometry : angle 0.65624 (15044) hydrogen bonds : bond 0.02890 ( 408) hydrogen bonds : angle 4.22728 ( 1167) metal coordination : bond 0.00545 ( 8) metal coordination : angle 5.30870 ( 9) Misc. bond : bond 0.00014 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1867.14 seconds wall clock time: 32 minutes 52.99 seconds (1972.99 seconds total)