Starting phenix.real_space_refine on Thu Feb 5 22:20:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qwx_53430/02_2026/9qwx_53430.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qwx_53430/02_2026/9qwx_53430.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 { model { file = "/net/cci-nas-00/data/ceres_data/9qwx_53430/02_2026/9qwx_53430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qwx_53430/02_2026/9qwx_53430.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qwx_53430/02_2026/9qwx_53430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qwx_53430/02_2026/9qwx_53430.map" } 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= -0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 12776 2.51 5 N 3438 2.21 5 O 3808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20114 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1351, 10057 Classifications: {'peptide': 1351} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1296} Chain breaks: 19 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 661 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 7, 'GLN:plan1': 11, 'HIS:plan': 5, 'ARG:plan': 4, 'TRP:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 237 Chain: "B" Number of atoms: 10057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1351, 10057 Classifications: {'peptide': 1351} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1296} Chain breaks: 19 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 661 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 7, 'GLN:plan1': 11, 'HIS:plan': 5, 'ARG:plan': 4, 'TRP:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 237 Time building chain proxies: 4.28, per 1000 atoms: 0.21 Number of scatterers: 20114 At special positions: 0 Unit cell: (238.384, 194.004, 152.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3808 8.00 N 3438 7.00 C 12776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 973.1 milliseconds 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 0 sheets defined 79.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.571A pdb=" N ALA A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.701A pdb=" N LEU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 removed outlier: 4.004A pdb=" N LEU A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 87 Processing helix chain 'A' and resid 97 through 117 Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 144 through 158 removed outlier: 4.171A pdb=" N THR A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.622A pdb=" N SER A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.816A pdb=" N LYS A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 280 removed outlier: 4.416A pdb=" N TYR A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.614A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 354 Processing helix chain 'A' and resid 365 through 395 Processing helix chain 'A' and resid 399 through 423 Processing helix chain 'A' and resid 427 through 433 Processing helix chain 'A' and resid 444 through 451 Processing helix chain 'A' and resid 470 through 493 removed outlier: 3.861A pdb=" N VAL A 493 " --> pdb=" O GLN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 528 Processing helix chain 'A' and resid 529 through 553 removed outlier: 3.508A pdb=" N LYS A 553 " --> pdb=" O GLN A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 662 Processing helix chain 'A' and resid 667 through 678 Processing helix chain 'A' and resid 679 through 697 Processing helix chain 'A' and resid 700 through 720 Processing helix chain 'A' and resid 724 through 736 Processing helix chain 'A' and resid 750 through 772 Processing helix chain 'A' and resid 776 through 797 removed outlier: 3.552A pdb=" N LEU A 780 " --> pdb=" O VAL A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 820 Processing helix chain 'A' and resid 822 through 841 removed outlier: 3.579A pdb=" N SER A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 853 through 868 Processing helix chain 'A' and resid 873 through 884 removed outlier: 3.620A pdb=" N PHE A 877 " --> pdb=" O PRO A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 923 Processing helix chain 'A' and resid 937 through 942 removed outlier: 3.926A pdb=" N GLU A 942 " --> pdb=" O GLU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 957 Processing helix chain 'A' and resid 962 through 973 Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 992 through 1011 Processing helix chain 'A' and resid 1016 through 1025 removed outlier: 4.475A pdb=" N MET A1025 " --> pdb=" O ASN A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1045 removed outlier: 3.745A pdb=" N ARG A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1060 removed outlier: 3.630A pdb=" N LYS A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1076 removed outlier: 3.827A pdb=" N SER A1076 " --> pdb=" O LEU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1102 Processing helix chain 'A' and resid 1117 through 1142 Processing helix chain 'A' and resid 1157 through 1180 removed outlier: 3.915A pdb=" N ALA A1161 " --> pdb=" O ASN A1157 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A1180 " --> pdb=" O TYR A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1204 removed outlier: 4.051A pdb=" N ILE A1204 " --> pdb=" O ALA A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1222 removed outlier: 4.440A pdb=" N THR A1217 " --> pdb=" O THR A1213 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A1222 " --> pdb=" O LEU A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1235 removed outlier: 3.857A pdb=" N THR A1228 " --> pdb=" O SER A1224 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL A1229 " --> pdb=" O SER A1225 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS A1230 " --> pdb=" O VAL A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1250 removed outlier: 3.768A pdb=" N ASN A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1272 removed outlier: 3.766A pdb=" N THR A1272 " --> pdb=" O ALA A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1275 No H-bonds generated for 'chain 'A' and resid 1273 through 1275' Processing helix chain 'A' and resid 1279 through 1302 removed outlier: 4.629A pdb=" N SER A1283 " --> pdb=" O PRO A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1319 Proline residue: A1316 - end of helix removed outlier: 3.676A pdb=" N LEU A1319 " --> pdb=" O LEU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1339 removed outlier: 3.665A pdb=" N ARG A1336 " --> pdb=" O ASN A1332 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1365 removed outlier: 4.349A pdb=" N ALA A1348 " --> pdb=" O ASP A1344 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS A1365 " --> pdb=" O ILE A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1390 removed outlier: 3.773A pdb=" N LEU A1377 " --> pdb=" O ASP A1373 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A1390 " --> pdb=" O LYS A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1404 removed outlier: 3.731A pdb=" N ALA A1396 " --> pdb=" O GLN A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1414 removed outlier: 4.210A pdb=" N ILE A1410 " --> pdb=" O GLU A1406 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A1411 " --> pdb=" O LEU A1407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A1414 " --> pdb=" O ILE A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1439 removed outlier: 4.046A pdb=" N CYS A1424 " --> pdb=" O SER A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1453 removed outlier: 3.583A pdb=" N LEU A1453 " --> pdb=" O LEU A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1457 removed outlier: 3.807A pdb=" N ALA A1457 " --> pdb=" O ALA A1454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1454 through 1457' Processing helix chain 'A' and resid 1460 through 1473 removed outlier: 3.534A pdb=" N MET A1471 " --> pdb=" O TRP A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1500 Processing helix chain 'A' and resid 1507 through 1529 removed outlier: 4.115A pdb=" N CYS A1511 " --> pdb=" O GLY A1507 " (cutoff:3.500A) Proline residue: A1520 - end of helix Processing helix chain 'A' and resid 1533 through 1546 removed outlier: 4.728A pdb=" N VAL A1539 " --> pdb=" O PRO A1535 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A1540 " --> pdb=" O GLU A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1572 removed outlier: 3.521A pdb=" N HIS A1557 " --> pdb=" O HIS A1553 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN A1558 " --> pdb=" O LEU A1554 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A1562 " --> pdb=" O ASN A1558 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER A1565 " --> pdb=" O VAL A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1581 Processing helix chain 'A' and resid 1589 through 1611 Processing helix chain 'B' and resid 29 through 40 Proline residue: B 35 - end of helix Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.624A pdb=" N LEU B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 removed outlier: 4.075A pdb=" N LEU B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 87 Processing helix chain 'B' and resid 97 through 117 Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 144 through 158 removed outlier: 4.238A pdb=" N THR B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.588A pdb=" N SER B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 Processing helix chain 'B' and resid 251 through 262 removed outlier: 3.859A pdb=" N LYS B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 280 removed outlier: 4.451A pdb=" N TYR B 269 " --> pdb=" O TYR B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 315 removed outlier: 3.718A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 354 Processing helix chain 'B' and resid 365 through 395 Processing helix chain 'B' and resid 399 through 423 Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 444 through 451 Processing helix chain 'B' and resid 470 through 493 removed outlier: 3.911A pdb=" N VAL B 493 " --> pdb=" O GLN B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 528 Processing helix chain 'B' and resid 529 through 553 Processing helix chain 'B' and resid 644 through 662 Processing helix chain 'B' and resid 667 through 678 Processing helix chain 'B' and resid 679 through 697 Processing helix chain 'B' and resid 700 through 720 Processing helix chain 'B' and resid 724 through 736 Processing helix chain 'B' and resid 750 through 772 Processing helix chain 'B' and resid 776 through 797 removed outlier: 3.563A pdb=" N LEU B 780 " --> pdb=" O VAL B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 820 Processing helix chain 'B' and resid 822 through 841 removed outlier: 3.529A pdb=" N SER B 841 " --> pdb=" O ILE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 853 through 868 Processing helix chain 'B' and resid 873 through 884 removed outlier: 3.740A pdb=" N PHE B 877 " --> pdb=" O PRO B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 923 Processing helix chain 'B' and resid 937 through 942 removed outlier: 3.824A pdb=" N GLU B 942 " --> pdb=" O GLU B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 957 Processing helix chain 'B' and resid 962 through 973 Processing helix chain 'B' and resid 974 through 976 No H-bonds generated for 'chain 'B' and resid 974 through 976' Processing helix chain 'B' and resid 977 through 982 removed outlier: 4.131A pdb=" N ASP B 981 " --> pdb=" O SER B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1011 Processing helix chain 'B' and resid 1016 through 1025 removed outlier: 4.680A pdb=" N MET B1025 " --> pdb=" O ASN B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1045 Processing helix chain 'B' and resid 1049 through 1060 removed outlier: 4.290A pdb=" N TRP B1053 " --> pdb=" O SER B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1076 removed outlier: 3.884A pdb=" N SER B1076 " --> pdb=" O LEU B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1102 Processing helix chain 'B' and resid 1117 through 1141 Processing helix chain 'B' and resid 1157 through 1180 removed outlier: 3.827A pdb=" N ALA B1161 " --> pdb=" O ASN B1157 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B1180 " --> pdb=" O TYR B1176 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1204 removed outlier: 3.923A pdb=" N ILE B1204 " --> pdb=" O ALA B1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1221 removed outlier: 4.576A pdb=" N THR B1217 " --> pdb=" O THR B1213 " (cutoff:3.500A) Processing helix chain 'B' and resid 1224 through 1235 removed outlier: 3.673A pdb=" N THR B1228 " --> pdb=" O SER B1224 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL B1229 " --> pdb=" O SER B1225 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS B1230 " --> pdb=" O VAL B1226 " (cutoff:3.500A) Processing helix chain 'B' and resid 1245 through 1250 removed outlier: 3.785A pdb=" N ASN B1249 " --> pdb=" O GLY B1245 " (cutoff:3.500A) Processing helix chain 'B' and resid 1256 through 1272 removed outlier: 3.708A pdb=" N THR B1272 " --> pdb=" O ALA B1268 " (cutoff:3.500A) Processing helix chain 'B' and resid 1273 through 1275 No H-bonds generated for 'chain 'B' and resid 1273 through 1275' Processing helix chain 'B' and resid 1279 through 1302 removed outlier: 4.478A pdb=" N SER B1283 " --> pdb=" O PRO B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1306 through 1320 removed outlier: 3.625A pdb=" N VAL B1310 " --> pdb=" O ASN B1306 " (cutoff:3.500A) Proline residue: B1316 - end of helix removed outlier: 3.890A pdb=" N LEU B1319 " --> pdb=" O LEU B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1326 through 1339 removed outlier: 3.683A pdb=" N ARG B1336 " --> pdb=" O ASN B1332 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE B1337 " --> pdb=" O SER B1333 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B1339 " --> pdb=" O GLU B1335 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1364 Processing helix chain 'B' and resid 1373 through 1390 removed outlier: 3.887A pdb=" N LEU B1377 " --> pdb=" O ASP B1373 " (cutoff:3.500A) Processing helix chain 'B' and resid 1390 through 1404 removed outlier: 3.778A pdb=" N ALA B1396 " --> pdb=" O GLN B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1407 through 1414 removed outlier: 3.875A pdb=" N MET B1411 " --> pdb=" O LEU B1407 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR B1414 " --> pdb=" O ILE B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1420 through 1439 removed outlier: 4.473A pdb=" N CYS B1424 " --> pdb=" O SER B1420 " (cutoff:3.500A) Processing helix chain 'B' and resid 1445 through 1453 removed outlier: 3.576A pdb=" N LEU B1453 " --> pdb=" O LEU B1449 " (cutoff:3.500A) Processing helix chain 'B' and resid 1454 through 1459 removed outlier: 3.542A pdb=" N ALA B1457 " --> pdb=" O ALA B1454 " (cutoff:3.500A) Processing helix chain 'B' and resid 1460 through 1473 removed outlier: 3.668A pdb=" N MET B1471 " --> pdb=" O TRP B1467 " (cutoff:3.500A) Processing helix chain 'B' and resid 1482 through 1500 Processing helix chain 'B' and resid 1507 through 1529 removed outlier: 3.935A pdb=" N CYS B1511 " --> pdb=" O GLY B1507 " (cutoff:3.500A) Proline residue: B1520 - end of helix Processing helix chain 'B' and resid 1533 through 1546 removed outlier: 3.518A pdb=" N LEU B1537 " --> pdb=" O GLY B1533 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET B1538 " --> pdb=" O PHE B1534 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL B1539 " --> pdb=" O PRO B1535 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL B1540 " --> pdb=" O GLU B1536 " (cutoff:3.500A) Processing helix chain 'B' and resid 1552 through 1572 removed outlier: 4.304A pdb=" N ASN B1558 " --> pdb=" O LEU B1554 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER B1565 " --> pdb=" O VAL B1561 " (cutoff:3.500A) Processing helix chain 'B' and resid 1573 through 1581 Processing helix chain 'B' and resid 1589 through 1611 1472 hydrogen bonds defined for protein. 4392 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: 3.16 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6647 1.34 - 1.46: 4232 1.46 - 1.58: 9429 1.58 - 1.70: 0 1.70 - 1.81: 138 Bond restraints: 20446 Sorted by residual: bond pdb=" CG LEU B 113 " pdb=" CD2 LEU B 113 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" CG LEU A 113 " pdb=" CD2 LEU A 113 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.76e+00 bond pdb=" C ASN A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.66e+00 bond pdb=" C ASN B 117 " pdb=" N PRO B 118 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.53e+00 bond pdb=" CA ILE B1236 " pdb=" CB ILE B1236 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.05e-02 9.07e+03 1.31e+00 ... (remaining 20441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 27628 3.41 - 6.82: 151 6.82 - 10.23: 18 10.23 - 13.64: 8 13.64 - 17.06: 1 Bond angle restraints: 27806 Sorted by residual: angle pdb=" CA LEU B 537 " pdb=" CB LEU B 537 " pdb=" CG LEU B 537 " ideal model delta sigma weight residual 116.30 133.36 -17.06 3.50e+00 8.16e-02 2.37e+01 angle pdb=" N VAL A 444 " pdb=" CA VAL A 444 " pdb=" C VAL A 444 " ideal model delta sigma weight residual 113.71 109.99 3.72 9.50e-01 1.11e+00 1.53e+01 angle pdb=" N VAL B 444 " pdb=" CA VAL B 444 " pdb=" C VAL B 444 " ideal model delta sigma weight residual 113.53 109.84 3.69 9.80e-01 1.04e+00 1.41e+01 angle pdb=" CA LEU A1434 " pdb=" CB LEU A1434 " pdb=" CG LEU A1434 " ideal model delta sigma weight residual 116.30 129.24 -12.94 3.50e+00 8.16e-02 1.37e+01 angle pdb=" CA LEU A1045 " pdb=" CB LEU A1045 " pdb=" CG LEU A1045 " ideal model delta sigma weight residual 116.30 128.71 -12.41 3.50e+00 8.16e-02 1.26e+01 ... (remaining 27801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10702 18.00 - 35.99: 1294 35.99 - 53.99: 282 53.99 - 71.98: 45 71.98 - 89.98: 27 Dihedral angle restraints: 12350 sinusoidal: 4412 harmonic: 7938 Sorted by residual: dihedral pdb=" CA ASN B 117 " pdb=" C ASN B 117 " pdb=" N PRO B 118 " pdb=" CA PRO B 118 " ideal model delta harmonic sigma weight residual 180.00 -131.73 -48.27 0 5.00e+00 4.00e-02 9.32e+01 dihedral pdb=" CA ASN A 117 " pdb=" C ASN A 117 " pdb=" N PRO A 118 " pdb=" CA PRO A 118 " ideal model delta harmonic sigma weight residual 180.00 -133.19 -46.81 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" CA MET B 285 " pdb=" C MET B 285 " pdb=" N PRO B 286 " pdb=" CA PRO B 286 " ideal model delta harmonic sigma weight residual 180.00 149.59 30.41 0 5.00e+00 4.00e-02 3.70e+01 ... (remaining 12347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2995 0.062 - 0.123: 328 0.123 - 0.185: 29 0.185 - 0.246: 6 0.246 - 0.308: 2 Chirality restraints: 3360 Sorted by residual: chirality pdb=" CG LEU A1381 " pdb=" CB LEU A1381 " pdb=" CD1 LEU A1381 " pdb=" CD2 LEU A1381 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CG LEU B 722 " pdb=" CB LEU B 722 " pdb=" CD1 LEU B 722 " pdb=" CD2 LEU B 722 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CG LEU A1284 " pdb=" CB LEU A1284 " pdb=" CD1 LEU A1284 " pdb=" CD2 LEU A1284 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3357 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 117 " -0.050 5.00e-02 4.00e+02 7.68e-02 9.45e+00 pdb=" N PRO A 118 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 117 " 0.047 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO B 118 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 202 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO A 203 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.034 5.00e-02 4.00e+02 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 10929 2.99 - 3.47: 23265 3.47 - 3.95: 31484 3.95 - 4.42: 36316 4.42 - 4.90: 55773 Nonbonded interactions: 157767 Sorted by model distance: nonbonded pdb=" O ASN A1239 " pdb=" OD1 ASN A1239 " model vdw 2.515 3.040 nonbonded pdb=" O GLN A1164 " pdb=" OD1 ASP A1167 " model vdw 2.517 3.040 nonbonded pdb=" N GLU B 319 " pdb=" OE1 GLU B 319 " model vdw 2.561 3.120 nonbonded pdb=" O GLU B 692 " pdb=" OE1 GLU B 692 " model vdw 2.564 3.040 nonbonded pdb=" O GLU A1328 " pdb=" OD1 ASN A1332 " model vdw 2.585 3.040 ... (remaining 157762 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=1.00 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: 3.460 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.030 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20446 Z= 0.134 Angle : 0.692 17.055 27806 Z= 0.347 Chirality : 0.041 0.308 3360 Planarity : 0.005 0.077 3552 Dihedral : 16.894 89.975 7142 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.55 % Favored : 96.30 % Rotamer: Outliers : 2.22 % Allowed : 20.95 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 2.83 % 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: 2.49 (0.17), residues: 2622 helix: 2.42 (0.12), residues: 1944 sheet: None (None), residues: 0 loop : -0.69 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 272 TYR 0.030 0.002 TYR B1122 PHE 0.035 0.002 PHE A 201 TRP 0.037 0.002 TRP B1041 HIS 0.006 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00289 (20446) covalent geometry : angle 0.69243 (27806) hydrogen bonds : bond 0.11845 ( 1472) hydrogen bonds : angle 4.64602 ( 4392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8194 (mt) cc_final: 0.7740 (tp) REVERT: A 285 MET cc_start: 0.5612 (ptt) cc_final: 0.4871 (tpt) REVERT: A 848 MET cc_start: 0.8342 (mmt) cc_final: 0.8058 (mpp) REVERT: A 912 LYS cc_start: 0.7643 (ptmm) cc_final: 0.7428 (ttpp) REVERT: B 84 TYR cc_start: 0.8735 (m-80) cc_final: 0.8416 (m-80) REVERT: B 285 MET cc_start: 0.6906 (pmm) cc_final: 0.5093 (tpt) REVERT: B 804 GLU cc_start: 0.7707 (tp30) cc_final: 0.7334 (tp30) REVERT: B 1314 LEU cc_start: 0.8749 (tt) cc_final: 0.8015 (pp) REVERT: B 1362 LEU cc_start: 0.8927 (mt) cc_final: 0.8724 (pp) outliers start: 46 outliers final: 41 residues processed: 219 average time/residue: 0.1215 time to fit residues: 45.1665 Evaluate side-chains 203 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 779 CYS Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 929 HIS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1000 GLN Chi-restraints excluded: chain B residue 1029 GLU Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1169 TYR Chi-restraints excluded: chain B residue 1425 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 GLN A1239 ASN B 728 GLN B 882 HIS B 990 ASN B1026 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.079612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.064598 restraints weight = 89905.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066242 restraints weight = 46798.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.067263 restraints weight = 31081.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.067919 restraints weight = 24148.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.068346 restraints weight = 20534.207| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20446 Z= 0.122 Angle : 0.608 13.372 27806 Z= 0.301 Chirality : 0.039 0.211 3360 Planarity : 0.004 0.082 3552 Dihedral : 6.058 56.034 2897 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.03 % Rotamer: Outliers : 3.23 % Allowed : 19.11 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 2.65 (0.17), residues: 2622 helix: 2.48 (0.12), residues: 1994 sheet: None (None), residues: 0 loop : -0.71 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 145 TYR 0.030 0.002 TYR B1122 PHE 0.029 0.001 PHE B 201 TRP 0.017 0.001 TRP B1041 HIS 0.007 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00266 (20446) covalent geometry : angle 0.60803 (27806) hydrogen bonds : bond 0.04082 ( 1472) hydrogen bonds : angle 3.63965 ( 4392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 171 time to evaluate : 0.515 Fit side-chains REVERT: A 167 LEU cc_start: 0.8188 (mt) cc_final: 0.7744 (tp) REVERT: A 285 MET cc_start: 0.5328 (ptt) cc_final: 0.4717 (tpp) REVERT: A 338 TYR cc_start: 0.7823 (t80) cc_final: 0.7565 (t80) REVERT: A 548 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8550 (tt) REVERT: A 912 LYS cc_start: 0.7789 (ptmm) cc_final: 0.7532 (ttpp) REVERT: A 1305 MET cc_start: 0.6124 (ttt) cc_final: 0.5852 (tmm) REVERT: A 1311 ILE cc_start: 0.9074 (pp) cc_final: 0.8871 (pp) REVERT: A 1381 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8305 (mt) REVERT: B 285 MET cc_start: 0.6827 (pmm) cc_final: 0.5125 (tpt) REVERT: B 548 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8603 (tt) REVERT: B 804 GLU cc_start: 0.7585 (tp30) cc_final: 0.6890 (tp30) REVERT: B 1314 LEU cc_start: 0.8682 (tt) cc_final: 0.7988 (pp) REVERT: B 1362 LEU cc_start: 0.8945 (mt) cc_final: 0.8732 (pp) outliers start: 67 outliers final: 35 residues processed: 235 average time/residue: 0.1156 time to fit residues: 45.5089 Evaluate side-chains 193 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 929 HIS Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1026 ASN Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1169 TYR Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 12 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.078984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.063813 restraints weight = 90659.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.065460 restraints weight = 47264.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.066510 restraints weight = 31498.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.067153 restraints weight = 24436.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067514 restraints weight = 20854.942| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20446 Z= 0.124 Angle : 0.599 10.770 27806 Z= 0.296 Chirality : 0.039 0.245 3360 Planarity : 0.004 0.085 3552 Dihedral : 5.307 56.941 2849 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % Rotamer: Outliers : 3.76 % Allowed : 19.35 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 2.71 (0.17), residues: 2622 helix: 2.51 (0.12), residues: 2010 sheet: None (None), residues: 0 loop : -0.73 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1293 TYR 0.031 0.002 TYR B1122 PHE 0.024 0.001 PHE B 201 TRP 0.039 0.001 TRP A1301 HIS 0.007 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00279 (20446) covalent geometry : angle 0.59866 (27806) hydrogen bonds : bond 0.03748 ( 1472) hydrogen bonds : angle 3.49496 ( 4392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 165 time to evaluate : 0.680 Fit side-chains REVERT: A 49 LEU cc_start: 0.9091 (mp) cc_final: 0.8657 (mp) REVERT: A 167 LEU cc_start: 0.8159 (mt) cc_final: 0.7854 (tp) REVERT: A 285 MET cc_start: 0.5646 (ptt) cc_final: 0.4930 (tpp) REVERT: A 548 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8532 (tt) REVERT: A 813 MET cc_start: 0.8823 (tmm) cc_final: 0.8441 (ttt) REVERT: A 912 LYS cc_start: 0.7888 (ptmm) cc_final: 0.7643 (ttpp) REVERT: A 1305 MET cc_start: 0.6123 (ttt) cc_final: 0.5687 (tmm) REVERT: A 1381 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8340 (mt) REVERT: B 548 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8591 (tt) REVERT: B 1025 MET cc_start: 0.7993 (pmm) cc_final: 0.7578 (pmm) REVERT: B 1036 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8787 (mt) REVERT: B 1362 LEU cc_start: 0.8964 (mt) cc_final: 0.8744 (pp) REVERT: B 1397 MET cc_start: 0.6758 (tmm) cc_final: 0.6490 (tmm) outliers start: 78 outliers final: 50 residues processed: 235 average time/residue: 0.1192 time to fit residues: 47.7724 Evaluate side-chains 204 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 TRP Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 929 HIS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1169 TYR Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1228 THR Chi-restraints excluded: chain B residue 1270 LEU Chi-restraints excluded: chain B residue 1273 LEU Chi-restraints excluded: chain B residue 1425 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 223 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 203 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 260 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 ASN ** B1067 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.077727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.062565 restraints weight = 90798.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064187 restraints weight = 47608.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065221 restraints weight = 31868.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.065849 restraints weight = 24779.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066234 restraints weight = 21268.094| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20446 Z= 0.134 Angle : 0.607 11.390 27806 Z= 0.299 Chirality : 0.039 0.221 3360 Planarity : 0.004 0.089 3552 Dihedral : 5.259 59.333 2845 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 4.30 % Allowed : 19.02 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 2.83 % 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: 2.80 (0.17), residues: 2622 helix: 2.61 (0.12), residues: 1996 sheet: None (None), residues: 0 loop : -0.75 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1293 TYR 0.029 0.002 TYR B1122 PHE 0.016 0.001 PHE B 201 TRP 0.050 0.002 TRP A1301 HIS 0.007 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00308 (20446) covalent geometry : angle 0.60728 (27806) hydrogen bonds : bond 0.03724 ( 1472) hydrogen bonds : angle 3.43456 ( 4392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 157 time to evaluate : 0.611 Fit side-chains REVERT: A 167 LEU cc_start: 0.8317 (mt) cc_final: 0.7900 (tt) REVERT: A 548 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8569 (tt) REVERT: A 833 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8901 (t80) REVERT: A 912 LYS cc_start: 0.7853 (ptmm) cc_final: 0.7614 (ttpp) REVERT: A 1135 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8267 (mt) REVERT: A 1305 MET cc_start: 0.6163 (ttt) cc_final: 0.5754 (tmm) REVERT: A 1381 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8457 (mt) REVERT: B 548 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8635 (tt) REVERT: B 1294 LEU cc_start: 0.9165 (tt) cc_final: 0.8959 (tp) REVERT: B 1314 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8358 (mt) REVERT: B 1329 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8436 (tp) REVERT: B 1362 LEU cc_start: 0.9019 (mt) cc_final: 0.8817 (pp) REVERT: B 1397 MET cc_start: 0.6637 (tmm) cc_final: 0.6388 (tmm) outliers start: 89 outliers final: 57 residues processed: 236 average time/residue: 0.1126 time to fit residues: 44.9187 Evaluate side-chains 211 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 147 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 TRP Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1210 LYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 929 HIS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1228 THR Chi-restraints excluded: chain B residue 1270 LEU Chi-restraints excluded: chain B residue 1314 LEU Chi-restraints excluded: chain B residue 1329 ILE Chi-restraints excluded: chain B residue 1425 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 65 optimal weight: 0.0050 chunk 209 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1026 ASN ** B1067 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.075299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.060121 restraints weight = 90422.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.061681 restraints weight = 47783.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.062650 restraints weight = 32317.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.063273 restraints weight = 25515.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.063653 restraints weight = 21908.417| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20446 Z= 0.178 Angle : 0.647 11.676 27806 Z= 0.326 Chirality : 0.041 0.247 3360 Planarity : 0.005 0.089 3552 Dihedral : 5.191 55.917 2841 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 4.78 % Allowed : 19.45 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 3.77 % 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: 2.75 (0.17), residues: 2622 helix: 2.56 (0.12), residues: 2000 sheet: None (None), residues: 0 loop : -0.73 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 142 TYR 0.030 0.002 TYR B1122 PHE 0.025 0.002 PHE B 201 TRP 0.064 0.002 TRP A1301 HIS 0.008 0.002 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00413 (20446) covalent geometry : angle 0.64715 (27806) hydrogen bonds : bond 0.04177 ( 1472) hydrogen bonds : angle 3.56847 ( 4392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 149 time to evaluate : 0.809 Fit side-chains REVERT: A 167 LEU cc_start: 0.8321 (mt) cc_final: 0.7828 (tt) REVERT: A 201 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.8074 (p90) REVERT: A 261 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8851 (mp) REVERT: A 304 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8791 (tp) REVERT: A 548 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8588 (tt) REVERT: A 833 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.9013 (t80) REVERT: A 1305 MET cc_start: 0.6417 (ttp) cc_final: 0.6021 (tmm) REVERT: A 1362 LEU cc_start: 0.9333 (pp) cc_final: 0.8880 (mt) REVERT: A 1381 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8442 (mt) REVERT: B 548 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8666 (tt) REVERT: B 844 MET cc_start: 0.8709 (tpt) cc_final: 0.8426 (tpt) REVERT: B 1025 MET cc_start: 0.8464 (pmm) cc_final: 0.8208 (pmm) REVERT: B 1329 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8518 (tp) REVERT: B 1397 MET cc_start: 0.6820 (tmm) cc_final: 0.6585 (tmm) outliers start: 99 outliers final: 58 residues processed: 239 average time/residue: 0.1216 time to fit residues: 49.6996 Evaluate side-chains 206 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 140 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1210 LYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 929 HIS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1228 THR Chi-restraints excluded: chain B residue 1270 LEU Chi-restraints excluded: chain B residue 1329 ILE Chi-restraints excluded: chain B residue 1425 ASN Chi-restraints excluded: chain B residue 1434 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 166 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1067 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.074555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059221 restraints weight = 90578.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060676 restraints weight = 50031.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.061606 restraints weight = 34974.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.062170 restraints weight = 27960.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.062549 restraints weight = 24489.509| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20446 Z= 0.197 Angle : 0.664 14.721 27806 Z= 0.330 Chirality : 0.041 0.243 3360 Planarity : 0.005 0.099 3552 Dihedral : 5.189 56.144 2839 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.50 % Favored : 95.46 % Rotamer: Outliers : 4.39 % Allowed : 20.66 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 3.77 % 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: 2.65 (0.17), residues: 2622 helix: 2.50 (0.11), residues: 2000 sheet: None (None), residues: 0 loop : -0.82 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1044 TYR 0.029 0.002 TYR B1122 PHE 0.024 0.002 PHE A1430 TRP 0.040 0.002 TRP A1301 HIS 0.008 0.002 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00460 (20446) covalent geometry : angle 0.66439 (27806) hydrogen bonds : bond 0.04245 ( 1472) hydrogen bonds : angle 3.62216 ( 4392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 145 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8278 (mt) cc_final: 0.7838 (tt) REVERT: A 285 MET cc_start: 0.6864 (ptt) cc_final: 0.6608 (ptt) REVERT: A 304 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8785 (tp) REVERT: A 548 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8752 (tt) REVERT: A 922 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6423 (m-80) REVERT: A 1305 MET cc_start: 0.6218 (ttp) cc_final: 0.5949 (tmm) REVERT: A 1362 LEU cc_start: 0.9347 (pp) cc_final: 0.8862 (mt) REVERT: A 1381 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8558 (mt) REVERT: B 548 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8711 (tt) REVERT: B 844 MET cc_start: 0.8663 (tpt) cc_final: 0.8366 (tpt) REVERT: B 1025 MET cc_start: 0.8532 (pmm) cc_final: 0.8178 (pmm) REVERT: B 1041 TRP cc_start: 0.6164 (t60) cc_final: 0.5356 (t60) REVERT: B 1329 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8609 (tp) outliers start: 91 outliers final: 62 residues processed: 228 average time/residue: 0.1258 time to fit residues: 49.0034 Evaluate side-chains 204 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 136 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 922 PHE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1210 LYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1301 TRP Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 929 HIS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1228 THR Chi-restraints excluded: chain B residue 1270 LEU Chi-restraints excluded: chain B residue 1329 ILE Chi-restraints excluded: chain B residue 1394 ARG Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1425 ASN Chi-restraints excluded: chain B residue 1434 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 99 optimal weight: 0.0770 chunk 161 optimal weight: 2.9990 chunk 186 optimal weight: 0.0000 chunk 192 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN ** A1387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.076630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.061638 restraints weight = 91094.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063261 restraints weight = 46781.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.064286 restraints weight = 31075.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.064944 restraints weight = 24124.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.065351 restraints weight = 20594.515| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20446 Z= 0.112 Angle : 0.617 14.487 27806 Z= 0.300 Chirality : 0.039 0.218 3360 Planarity : 0.005 0.093 3552 Dihedral : 5.004 56.531 2839 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 3.23 % Allowed : 21.86 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 2.83 % 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: 2.88 (0.17), residues: 2622 helix: 2.67 (0.12), residues: 2000 sheet: None (None), residues: 0 loop : -0.75 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1293 TYR 0.028 0.002 TYR B1122 PHE 0.036 0.001 PHE A1430 TRP 0.034 0.002 TRP A1301 HIS 0.006 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00245 (20446) covalent geometry : angle 0.61708 (27806) hydrogen bonds : bond 0.03491 ( 1472) hydrogen bonds : angle 3.34067 ( 4392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 156 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8218 (mt) cc_final: 0.7820 (tt) REVERT: A 304 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8708 (tp) REVERT: A 548 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8541 (tt) REVERT: A 848 MET cc_start: 0.8235 (mmt) cc_final: 0.8017 (mmm) REVERT: A 1305 MET cc_start: 0.6183 (ttp) cc_final: 0.5916 (tmm) REVERT: A 1381 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8824 (mt) REVERT: B 548 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8618 (tt) REVERT: B 760 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8827 (mp) REVERT: B 1025 MET cc_start: 0.8642 (pmm) cc_final: 0.8302 (pmm) REVERT: B 1041 TRP cc_start: 0.6173 (t60) cc_final: 0.5422 (t60) REVERT: B 1362 LEU cc_start: 0.9084 (mt) cc_final: 0.8858 (pp) outliers start: 67 outliers final: 45 residues processed: 219 average time/residue: 0.1158 time to fit residues: 43.0875 Evaluate side-chains 197 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1301 TRP Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 929 HIS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1270 LEU Chi-restraints excluded: chain B residue 1354 LEU Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1425 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 187 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 HIS ** A1387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.074651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.059512 restraints weight = 88245.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.060979 restraints weight = 46446.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.060963 restraints weight = 31070.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.061096 restraints weight = 30280.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061261 restraints weight = 29560.912| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20446 Z= 0.175 Angle : 0.658 14.966 27806 Z= 0.322 Chirality : 0.041 0.251 3360 Planarity : 0.005 0.098 3552 Dihedral : 5.082 55.942 2839 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 3.52 % Allowed : 21.81 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 3.77 % 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: 2.81 (0.17), residues: 2622 helix: 2.61 (0.11), residues: 2002 sheet: None (None), residues: 0 loop : -0.77 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 450 TYR 0.027 0.002 TYR B1122 PHE 0.033 0.002 PHE A1430 TRP 0.036 0.002 TRP A1301 HIS 0.007 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00409 (20446) covalent geometry : angle 0.65794 (27806) hydrogen bonds : bond 0.04056 ( 1472) hydrogen bonds : angle 3.50873 ( 4392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 137 time to evaluate : 0.842 Fit side-chains REVERT: A 167 LEU cc_start: 0.8320 (mt) cc_final: 0.7821 (tt) REVERT: A 304 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8776 (tp) REVERT: A 548 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8502 (tt) REVERT: A 791 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8977 (tttp) REVERT: A 848 MET cc_start: 0.8330 (mmt) cc_final: 0.8104 (mmm) REVERT: A 922 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: A 947 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.4716 (tpm170) REVERT: A 1305 MET cc_start: 0.6547 (ttp) cc_final: 0.6195 (tmm) REVERT: A 1381 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8748 (mt) REVERT: B 548 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8552 (tt) REVERT: B 760 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8841 (mp) REVERT: B 1025 MET cc_start: 0.8808 (pmm) cc_final: 0.8406 (pmm) outliers start: 73 outliers final: 53 residues processed: 202 average time/residue: 0.1286 time to fit residues: 43.8140 Evaluate side-chains 200 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 139 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 922 PHE Chi-restraints excluded: chain A residue 947 ARG Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 TRP Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1301 TRP Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1270 LEU Chi-restraints excluded: chain B residue 1354 LEU Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1425 ASN Chi-restraints excluded: chain B residue 1434 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 86 optimal weight: 1.9990 chunk 247 optimal weight: 0.0470 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 189 optimal weight: 0.6980 chunk 269 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.075872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.060467 restraints weight = 87793.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062560 restraints weight = 48311.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.062792 restraints weight = 28096.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.062993 restraints weight = 26052.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063488 restraints weight = 23969.812| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20446 Z= 0.120 Angle : 0.629 15.921 27806 Z= 0.304 Chirality : 0.039 0.241 3360 Planarity : 0.005 0.095 3552 Dihedral : 4.928 56.665 2837 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 2.99 % Allowed : 22.59 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 3.77 % 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: 2.89 (0.17), residues: 2622 helix: 2.68 (0.11), residues: 2000 sheet: None (None), residues: 0 loop : -0.74 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 450 TYR 0.027 0.002 TYR B1122 PHE 0.032 0.001 PHE A1430 TRP 0.034 0.002 TRP A1301 HIS 0.006 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00269 (20446) covalent geometry : angle 0.62929 (27806) hydrogen bonds : bond 0.03609 ( 1472) hydrogen bonds : angle 3.38301 ( 4392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 144 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8290 (mt) cc_final: 0.7829 (tt) REVERT: A 304 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8736 (tp) REVERT: A 548 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8535 (tt) REVERT: A 848 MET cc_start: 0.8292 (mmt) cc_final: 0.8033 (mmm) REVERT: A 922 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6583 (m-80) REVERT: A 947 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.4586 (tpm170) REVERT: A 1305 MET cc_start: 0.6360 (ttp) cc_final: 0.6149 (tmm) REVERT: A 1381 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8735 (mt) REVERT: B 131 LEU cc_start: 0.9117 (mp) cc_final: 0.8785 (mt) REVERT: B 548 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8595 (tt) REVERT: B 760 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8838 (mp) REVERT: B 1025 MET cc_start: 0.8788 (pmm) cc_final: 0.8444 (pmm) outliers start: 62 outliers final: 49 residues processed: 200 average time/residue: 0.1270 time to fit residues: 42.7907 Evaluate side-chains 198 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 922 PHE Chi-restraints excluded: chain A residue 947 ARG Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1301 TRP Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1270 LEU Chi-restraints excluded: chain B residue 1354 LEU Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1425 ASN Chi-restraints excluded: chain B residue 1434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 53 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.075312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060276 restraints weight = 88493.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.061972 restraints weight = 42434.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.062306 restraints weight = 27328.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062539 restraints weight = 26095.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.062655 restraints weight = 23493.009| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20446 Z= 0.137 Angle : 0.640 15.861 27806 Z= 0.308 Chirality : 0.040 0.249 3360 Planarity : 0.005 0.097 3552 Dihedral : 4.910 57.011 2837 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 3.19 % Allowed : 22.39 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 3.77 % 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: 2.89 (0.17), residues: 2622 helix: 2.68 (0.11), residues: 2002 sheet: None (None), residues: 0 loop : -0.78 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 450 TYR 0.027 0.002 TYR B1122 PHE 0.051 0.001 PHE B1431 TRP 0.035 0.002 TRP A1301 HIS 0.006 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00318 (20446) covalent geometry : angle 0.63981 (27806) hydrogen bonds : bond 0.03688 ( 1472) hydrogen bonds : angle 3.40249 ( 4392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 142 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8314 (mt) cc_final: 0.7807 (tt) REVERT: A 304 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8753 (tp) REVERT: A 548 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8503 (tt) REVERT: A 848 MET cc_start: 0.8287 (mmt) cc_final: 0.8018 (mmm) REVERT: A 922 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: A 947 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.4754 (tpm170) REVERT: A 1305 MET cc_start: 0.6391 (ttp) cc_final: 0.6156 (tmm) REVERT: A 1381 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8747 (mt) REVERT: A 1430 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.8016 (t80) REVERT: B 131 LEU cc_start: 0.9116 (mp) cc_final: 0.8791 (mt) REVERT: B 548 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8585 (tt) REVERT: B 760 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8822 (mp) REVERT: B 1025 MET cc_start: 0.8823 (pmm) cc_final: 0.8473 (pmm) REVERT: B 1419 LEU cc_start: 0.8243 (tp) cc_final: 0.8042 (tp) REVERT: B 1431 PHE cc_start: 0.8366 (m-80) cc_final: 0.8153 (m-80) outliers start: 66 outliers final: 54 residues processed: 200 average time/residue: 0.1259 time to fit residues: 41.9340 Evaluate side-chains 202 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 140 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 922 PHE Chi-restraints excluded: chain A residue 947 ARG Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1210 LYS Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1301 TRP Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1430 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 829 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1270 LEU Chi-restraints excluded: chain B residue 1354 LEU Chi-restraints excluded: chain B residue 1408 VAL Chi-restraints excluded: chain B residue 1425 ASN Chi-restraints excluded: chain B residue 1434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 100 optimal weight: 0.8980 chunk 236 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 269 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 chunk 46 optimal weight: 0.8980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.076213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.060873 restraints weight = 87744.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.063111 restraints weight = 45307.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.063361 restraints weight = 27207.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063688 restraints weight = 25658.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063761 restraints weight = 22606.555| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20446 Z= 0.114 Angle : 0.628 16.373 27806 Z= 0.299 Chirality : 0.039 0.256 3360 Planarity : 0.005 0.095 3552 Dihedral : 4.847 57.323 2837 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 3.09 % Allowed : 22.59 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 3.77 % 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: 2.93 (0.17), residues: 2622 helix: 2.71 (0.11), residues: 2002 sheet: None (None), residues: 0 loop : -0.77 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 450 TYR 0.027 0.001 TYR B1122 PHE 0.040 0.001 PHE B1431 TRP 0.033 0.002 TRP A1301 HIS 0.006 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00257 (20446) covalent geometry : angle 0.62846 (27806) hydrogen bonds : bond 0.03406 ( 1472) hydrogen bonds : angle 3.31791 ( 4392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3515.90 seconds wall clock time: 61 minutes 30.53 seconds (3690.53 seconds total)