Starting phenix.real_space_refine on Tue May 13 19:34:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x6v_33028/05_2025/7x6v_33028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x6v_33028/05_2025/7x6v_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_33028/05_2025/7x6v_33028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x6v_33028/05_2025/7x6v_33028.map" model { file = "/net/cci-nas-00/data/ceres_data/7x6v_33028/05_2025/7x6v_33028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x6v_33028/05_2025/7x6v_33028.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 23} 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: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 23} 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: 11.12, per 1000 atoms: 1.02 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: 2.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.27 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: 3.43 Time building geometry restraints manager: 3.06 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.270 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.070 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.200 ------------------------------------------------------------------------------- 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 : 15.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.003 TRP B 36 HIS 0.009 0.002 HIS A 561 PHE 0.042 0.003 PHE A 299 TYR 0.022 0.003 TYR A1803 ARG 0.010 0.001 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.17195 ( 408) hydrogen bonds : angle 7.43674 ( 1167) metal coordination : bond 0.22240 ( 8) metal coordination : angle 17.81842 ( 9) covalent geometry : bond 0.01065 (11114) covalent geometry : angle 1.51597 (15044) 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 : 1.294 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: 0.2678 (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: 0.2438 time to fit residues: 70.6559 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 : 1.270 ------------------------------------------------------------------------------- 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 119 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 30.0000 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.202833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.156119 restraints weight = 21331.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.159596 restraints weight = 12208.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.159898 restraints weight = 7749.506| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11123 Z= 0.157 Angle : 0.824 15.796 15053 Z= 0.413 Chirality : 0.047 0.279 1711 Planarity : 0.005 0.072 1943 Dihedral : 6.536 44.871 1517 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.29 % Favored : 88.56 % Rotamer: Outliers : 1.33 % Allowed : 9.68 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.21), residues: 1400 helix: -1.02 (0.19), residues: 688 sheet: -1.96 (0.69), residues: 65 loop : -3.68 (0.21), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1223 HIS 0.012 0.001 HIS A1492 PHE 0.034 0.002 PHE A1390 TYR 0.021 0.002 TYR A 745 ARG 0.008 0.001 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 408) hydrogen bonds : angle 5.27460 ( 1167) metal coordination : bond 0.01855 ( 8) metal coordination : angle 7.28273 ( 9) covalent geometry : bond 0.00330 (11114) covalent geometry : angle 0.80467 (15044) Misc. bond : bond 0.00134 ( 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 162 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8106 (pt) cc_final: 0.7822 (pt) REVERT: A 1498 GLU cc_start: 0.6392 (tp30) cc_final: 0.5622 (mp0) REVERT: A 1654 TYR cc_start: 0.5253 (m-80) cc_final: 0.2823 (m-80) REVERT: A 1807 PHE cc_start: 0.8210 (t80) cc_final: 0.7909 (t80) outliers start: 15 outliers final: 10 residues processed: 156 average time/residue: 0.2043 time to fit residues: 47.4860 Evaluate side-chains 136 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER 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 532 ILE 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 1492 HIS 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 133 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 111 optimal weight: 0.0570 chunk 140 optimal weight: 5.9990 overall best weight: 1.2702 ------------------------------------------------------------------------------- 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 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN A1492 HIS A1686 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.196722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.149361 restraints weight = 18486.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.147776 restraints weight = 12253.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.150158 restraints weight = 8475.539| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4021 r_free = 0.4021 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4021 r_free = 0.4021 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11123 Z= 0.151 Angle : 0.749 13.507 15053 Z= 0.377 Chirality : 0.045 0.373 1711 Planarity : 0.005 0.071 1943 Dihedral : 5.988 32.708 1513 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.01 % Favored : 87.85 % Rotamer: Outliers : 1.42 % Allowed : 11.28 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.21), residues: 1400 helix: -0.80 (0.19), residues: 682 sheet: -2.09 (0.61), residues: 77 loop : -3.49 (0.21), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1223 HIS 0.032 0.002 HIS A1492 PHE 0.051 0.002 PHE A 720 TYR 0.015 0.001 TYR A 745 ARG 0.006 0.000 ARG A1464 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 408) hydrogen bonds : angle 4.96449 ( 1167) metal coordination : bond 0.00371 ( 8) metal coordination : angle 6.20535 ( 9) covalent geometry : bond 0.00334 (11114) covalent geometry : angle 0.73379 (15044) Misc. bond : bond 0.00047 ( 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 : 1.174 Fit side-chains REVERT: A 185 ARG cc_start: 0.6623 (mpt180) cc_final: 0.5201 (mtm180) REVERT: A 205 ILE cc_start: 0.8226 (pt) cc_final: 0.7948 (pt) REVERT: A 323 MET cc_start: 0.6312 (mmm) cc_final: 0.5615 (mpp) REVERT: A 1134 MET cc_start: 0.7991 (tpp) cc_final: 0.7594 (tpp) REVERT: A 1498 GLU cc_start: 0.6366 (tp30) cc_final: 0.5664 (mp0) REVERT: A 1576 ASN cc_start: 0.9205 (t0) cc_final: 0.8931 (t0) REVERT: A 1807 PHE cc_start: 0.8200 (t80) cc_final: 0.7956 (t80) outliers start: 16 outliers final: 9 residues processed: 139 average time/residue: 0.1972 time to fit residues: 41.1580 Evaluate side-chains 126 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASN 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 1452 THR Chi-restraints excluded: chain A residue 1492 HIS 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 54 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 3 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 0.0010 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 A 561 HIS A1208 GLN A1492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.192197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.143780 restraints weight = 18748.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.141503 restraints weight = 12554.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.142933 restraints weight = 11105.035| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11123 Z= 0.154 Angle : 0.733 17.008 15053 Z= 0.366 Chirality : 0.044 0.205 1711 Planarity : 0.005 0.073 1943 Dihedral : 5.750 31.806 1512 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.58 % Favored : 88.28 % Rotamer: Outliers : 1.69 % Allowed : 13.50 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.22), residues: 1400 helix: -0.58 (0.20), residues: 688 sheet: -2.07 (0.61), residues: 80 loop : -3.30 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 36 HIS 0.022 0.002 HIS A1492 PHE 0.025 0.002 PHE A 720 TYR 0.017 0.001 TYR A 543 ARG 0.007 0.000 ARG A1330 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 408) hydrogen bonds : angle 4.85390 ( 1167) metal coordination : bond 0.01048 ( 8) metal coordination : angle 7.63163 ( 9) covalent geometry : bond 0.00337 (11114) covalent geometry : angle 0.70954 (15044) Misc. bond : bond 0.00059 ( 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 137 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.305 Fit side-chains REVERT: A 205 ILE cc_start: 0.8404 (pt) cc_final: 0.8123 (pt) REVERT: A 323 MET cc_start: 0.6528 (mmm) cc_final: 0.6057 (tpp) REVERT: A 464 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.5604 (ppp) REVERT: A 770 PHE cc_start: 0.8714 (t80) cc_final: 0.8482 (t80) REVERT: A 1134 MET cc_start: 0.8069 (tpp) cc_final: 0.7613 (tpp) REVERT: A 1328 ASP cc_start: 0.7462 (t0) cc_final: 0.7155 (t0) REVERT: A 1338 ASP cc_start: 0.7083 (t70) cc_final: 0.6760 (t0) REVERT: A 1452 THR cc_start: 0.8916 (m) cc_final: 0.8632 (m) REVERT: A 1498 GLU cc_start: 0.6416 (tp30) cc_final: 0.5855 (mp0) REVERT: A 1576 ASN cc_start: 0.9291 (t0) cc_final: 0.9020 (t0) REVERT: A 1807 PHE cc_start: 0.8247 (t80) cc_final: 0.8024 (t80) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 0.1839 time to fit residues: 36.9928 Evaluate side-chains 118 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 445 CYS 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 1271 ILE Chi-restraints excluded: chain A residue 1412 THR Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1777 LEU 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 85 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 56 optimal weight: 0.0060 chunk 59 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 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 = 0.4487 r_free = 0.4487 target = 0.194288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.143268 restraints weight = 31331.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.143591 restraints weight = 13454.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.145414 restraints weight = 10865.474| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11123 Z= 0.114 Angle : 0.687 14.465 15053 Z= 0.342 Chirality : 0.042 0.192 1711 Planarity : 0.004 0.071 1943 Dihedral : 5.450 30.386 1512 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.94 % Favored : 89.92 % Rotamer: Outliers : 1.33 % Allowed : 15.19 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.22), residues: 1400 helix: -0.41 (0.20), residues: 701 sheet: -1.96 (0.60), residues: 80 loop : -3.24 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1223 HIS 0.025 0.001 HIS A 561 PHE 0.020 0.001 PHE A1508 TYR 0.014 0.001 TYR A 745 ARG 0.004 0.000 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 408) hydrogen bonds : angle 4.65833 ( 1167) metal coordination : bond 0.00462 ( 8) metal coordination : angle 6.41983 ( 9) covalent geometry : bond 0.00241 (11114) covalent geometry : angle 0.66945 (15044) Misc. bond : bond 0.00005 ( 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 133 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.145 Fit side-chains REVERT: A 205 ILE cc_start: 0.8429 (pt) cc_final: 0.8198 (pt) REVERT: A 464 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5568 (ppp) REVERT: A 1134 MET cc_start: 0.7938 (tpp) cc_final: 0.7659 (tpp) REVERT: A 1328 ASP cc_start: 0.7332 (t0) cc_final: 0.6975 (t0) REVERT: A 1332 SER cc_start: 0.9237 (t) cc_final: 0.8510 (p) REVERT: A 1338 ASP cc_start: 0.7154 (t70) cc_final: 0.6933 (t0) REVERT: A 1452 THR cc_start: 0.8679 (m) cc_final: 0.8353 (m) REVERT: A 1498 GLU cc_start: 0.6472 (tp30) cc_final: 0.5751 (mp0) REVERT: A 1576 ASN cc_start: 0.9262 (t0) cc_final: 0.9004 (t0) REVERT: A 1807 PHE cc_start: 0.8255 (t80) cc_final: 0.7985 (t80) outliers start: 15 outliers final: 9 residues processed: 126 average time/residue: 0.1809 time to fit residues: 35.1869 Evaluate side-chains 118 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 493 VAL 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 1523 LEU Chi-restraints excluded: chain A residue 1777 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 25 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 0.0570 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- 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 334 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 561 HIS A1208 GLN A1492 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.186301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.135318 restraints weight = 18503.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.136351 restraints weight = 11961.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.136671 restraints weight = 9277.666| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11123 Z= 0.170 Angle : 0.739 15.209 15053 Z= 0.369 Chirality : 0.044 0.190 1711 Planarity : 0.005 0.074 1943 Dihedral : 5.618 29.634 1512 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.87 % Favored : 86.99 % Rotamer: Outliers : 1.51 % Allowed : 16.43 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.22), residues: 1400 helix: -0.41 (0.20), residues: 699 sheet: -2.06 (0.60), residues: 81 loop : -3.18 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1186 HIS 0.014 0.001 HIS A 561 PHE 0.026 0.002 PHE A 299 TYR 0.016 0.001 TYR A 543 ARG 0.005 0.000 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 408) hydrogen bonds : angle 4.73578 ( 1167) metal coordination : bond 0.00517 ( 8) metal coordination : angle 6.56923 ( 9) covalent geometry : bond 0.00392 (11114) covalent geometry : angle 0.72111 (15044) Misc. bond : bond 0.00069 ( 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 131 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.170 Fit side-chains REVERT: A 104 PHE cc_start: 0.7662 (p90) cc_final: 0.7364 (p90) REVERT: A 205 ILE cc_start: 0.8766 (pt) cc_final: 0.8558 (pt) REVERT: A 464 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5262 (ppp) REVERT: A 1134 MET cc_start: 0.8001 (tpp) cc_final: 0.7700 (tpp) REVERT: A 1338 ASP cc_start: 0.7391 (t70) cc_final: 0.7180 (t0) REVERT: A 1498 GLU cc_start: 0.6441 (tp30) cc_final: 0.6180 (mp0) REVERT: A 1576 ASN cc_start: 0.9259 (t0) cc_final: 0.8990 (t0) REVERT: A 1807 PHE cc_start: 0.8396 (t80) cc_final: 0.8136 (t80) REVERT: A 1808 SER cc_start: 0.8202 (t) cc_final: 0.7869 (t) outliers start: 17 outliers final: 6 residues processed: 123 average time/residue: 0.1825 time to fit residues: 34.8338 Evaluate side-chains 110 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1412 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 36 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 540 HIS A 561 HIS A1208 GLN A1492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.181964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.132157 restraints weight = 29574.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.133490 restraints weight = 11772.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.135485 restraints weight = 8865.697| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11123 Z= 0.139 Angle : 0.697 14.463 15053 Z= 0.349 Chirality : 0.043 0.218 1711 Planarity : 0.005 0.072 1943 Dihedral : 5.464 29.757 1512 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.58 % Favored : 89.28 % Rotamer: Outliers : 0.98 % Allowed : 17.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.22), residues: 1400 helix: -0.25 (0.20), residues: 698 sheet: -1.86 (0.60), residues: 79 loop : -3.12 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1537 HIS 0.026 0.001 HIS A 561 PHE 0.019 0.001 PHE A1508 TYR 0.017 0.001 TYR A1266 ARG 0.009 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 408) hydrogen bonds : angle 4.60758 ( 1167) metal coordination : bond 0.00492 ( 8) metal coordination : angle 6.20342 ( 9) covalent geometry : bond 0.00320 (11114) covalent geometry : angle 0.68054 (15044) Misc. bond : bond 0.00032 ( 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 114 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.155 Fit side-chains REVERT: A 200 MET cc_start: 0.7576 (ttp) cc_final: 0.6785 (pmm) REVERT: A 464 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5615 (ppp) REVERT: A 1134 MET cc_start: 0.7848 (tpp) cc_final: 0.7571 (tpp) REVERT: A 1332 SER cc_start: 0.9162 (t) cc_final: 0.8513 (p) REVERT: A 1338 ASP cc_start: 0.7319 (t70) cc_final: 0.7113 (t0) REVERT: A 1452 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8370 (m) REVERT: A 1498 GLU cc_start: 0.6477 (tp30) cc_final: 0.6188 (mp0) REVERT: A 1576 ASN cc_start: 0.9244 (t0) cc_final: 0.8986 (t0) REVERT: A 1807 PHE cc_start: 0.8362 (t80) cc_final: 0.8127 (t80) outliers start: 11 outliers final: 8 residues processed: 109 average time/residue: 0.1940 time to fit residues: 32.2300 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 : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 464 MET 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 1412 THR Chi-restraints excluded: chain A residue 1452 THR 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 114 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 0.0370 chunk 124 optimal weight: 0.0050 overall best weight: 0.7474 ------------------------------------------------------------------------------- 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** A1122 ASN 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 = 0.4187 r_free = 0.4187 target = 0.174889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119744 restraints weight = 20147.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124573 restraints weight = 9540.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127736 restraints weight = 6053.247| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 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 = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11123 Z= 0.119 Angle : 0.676 13.215 15053 Z= 0.338 Chirality : 0.042 0.198 1711 Planarity : 0.004 0.072 1943 Dihedral : 5.212 29.769 1512 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.36 % Favored : 89.49 % Rotamer: Outliers : 1.15 % Allowed : 17.76 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.22), residues: 1400 helix: -0.01 (0.20), residues: 692 sheet: -1.81 (0.59), residues: 81 loop : -3.01 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1537 HIS 0.009 0.001 HIS A1492 PHE 0.022 0.001 PHE A 112 TYR 0.015 0.001 TYR A 745 ARG 0.010 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 408) hydrogen bonds : angle 4.43906 ( 1167) metal coordination : bond 0.00501 ( 8) metal coordination : angle 5.68714 ( 9) covalent geometry : bond 0.00263 (11114) covalent geometry : angle 0.66124 (15044) Misc. bond : bond 0.00015 ( 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: 13 poor density : 108 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.7523 (ttp) cc_final: 0.6713 (pmm) REVERT: A 464 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5630 (ppp) REVERT: A 745 TYR cc_start: 0.7473 (m-10) cc_final: 0.6776 (m-10) REVERT: A 1134 MET cc_start: 0.8006 (tpp) cc_final: 0.7527 (tpp) REVERT: A 1332 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8348 (p) REVERT: A 1338 ASP cc_start: 0.7472 (t70) cc_final: 0.6852 (t0) REVERT: A 1452 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8191 (m) REVERT: A 1807 PHE cc_start: 0.8434 (t80) cc_final: 0.8169 (t80) outliers start: 13 outliers final: 7 residues processed: 116 average time/residue: 0.1942 time to fit residues: 34.6953 Evaluate side-chains 104 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 445 CYS Chi-restraints excluded: chain A residue 464 MET 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 1332 SER Chi-restraints excluded: chain A residue 1452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.035 > 50: distance: 54 - 57: 33.784 distance: 57 - 58: 40.150 distance: 58 - 59: 60.059 distance: 59 - 60: 18.211 distance: 59 - 61: 44.067 distance: 61 - 62: 29.935 distance: 62 - 63: 27.112 distance: 62 - 65: 49.869 distance: 63 - 64: 10.604 distance: 63 - 67: 51.565 distance: 65 - 66: 63.983 distance: 67 - 68: 7.936 distance: 68 - 69: 41.216 distance: 68 - 71: 41.981 distance: 69 - 70: 30.563 distance: 69 - 72: 28.817 distance: 72 - 73: 3.535 distance: 73 - 74: 9.667 distance: 73 - 76: 55.065 distance: 74 - 75: 54.836 distance: 74 - 78: 36.257 distance: 76 - 77: 49.422 distance: 78 - 79: 26.196 distance: 79 - 80: 26.203 distance: 79 - 82: 25.643 distance: 80 - 81: 16.853 distance: 80 - 85: 44.179 distance: 81 - 145: 29.802 distance: 82 - 83: 43.254 distance: 82 - 84: 41.558 distance: 85 - 86: 33.297 distance: 86 - 87: 41.227 distance: 86 - 89: 42.119 distance: 87 - 88: 54.807 distance: 87 - 96: 7.563 distance: 89 - 90: 28.421 distance: 90 - 91: 51.257 distance: 91 - 92: 21.696 distance: 92 - 93: 10.772 distance: 93 - 94: 24.090 distance: 93 - 95: 11.072 distance: 96 - 97: 45.176 distance: 97 - 98: 28.999 distance: 97 - 100: 8.606 distance: 98 - 99: 35.161 distance: 98 - 104: 17.076 distance: 100 - 101: 51.373 distance: 101 - 102: 32.248 distance: 101 - 103: 12.218 distance: 104 - 105: 8.386 distance: 105 - 106: 36.128 distance: 105 - 108: 3.949 distance: 106 - 107: 14.704 distance: 106 - 113: 24.724 distance: 108 - 109: 24.083 distance: 109 - 110: 23.420 distance: 110 - 111: 18.957 distance: 111 - 112: 43.033 distance: 113 - 114: 5.777 distance: 114 - 115: 43.308 distance: 114 - 117: 38.937 distance: 115 - 116: 9.074 distance: 115 - 121: 19.229 distance: 117 - 118: 7.813 distance: 118 - 119: 30.911 distance: 118 - 120: 27.575 distance: 121 - 122: 20.821 distance: 122 - 123: 12.270 distance: 122 - 125: 14.341 distance: 123 - 124: 16.804 distance: 123 - 132: 23.747 distance: 125 - 126: 17.128 distance: 126 - 127: 31.185 distance: 127 - 128: 15.629 distance: 128 - 129: 16.470 distance: 129 - 130: 21.515 distance: 129 - 131: 36.476