Starting phenix.real_space_refine on Sat Aug 8 18:40:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hf0_34707/08_2026/8hf0_34707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf0_34707/08_2026/8hf0_34707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hf0_34707/08_2026/8hf0_34707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf0_34707/08_2026/8hf0_34707.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hf0_34707/08_2026/8hf0_34707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hf0_34707/08_2026/8hf0_34707.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hf0_34707/08_2026/8hf0_34707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf0_34707/08_2026/8hf0_34707.cif" } resolution = 3.72 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= 0.007 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 153 5.16 5 C 18503 2.51 5 N 5028 2.21 5 O 5729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29510 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 12634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1561, 12634 Classifications: {'peptide': 1561} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 1495} Chain breaks: 2 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1027 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "D" Number of atoms: 12634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1561, 12634 Classifications: {'peptide': 1561} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 1495} Chain breaks: 2 Chain: "E" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1010 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "P" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1003 Classifications: {'RNAv2': 47} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 25, 'rna3p_pyr': 21} Link IDs: {'rna3p': 46} Chain: "N" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1058 Classifications: {'RNAv2': 50} Modifications used: {'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna3p': 49} Time building chain proxies: 5.91, per 1000 atoms: 0.20 Number of scatterers: 29510 At special positions: 0 Unit cell: (160.056, 174.02, 183.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 153 16.00 P 97 15.00 O 5729 8.00 N 5028 7.00 C 18503 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: 2.56 Conformation dependent library (CDL) restraints added in 1.3 seconds 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6488 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 26 sheets defined 55.3% alpha, 11.7% beta 42 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 Processing helix chain 'A' and resid 31 through 45 removed outlier: 4.082A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.588A pdb=" N PHE A 49 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP A 50 " --> pdb=" O GLN A 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 50' Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 148 through 156 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.592A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.609A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 removed outlier: 3.644A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 Processing helix chain 'A' and resid 316 through 345 removed outlier: 3.642A pdb=" N MET A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.606A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.858A pdb=" N ALA A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 535 removed outlier: 3.633A pdb=" N THR A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 582 Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 608 through 611 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 667 through 680 removed outlier: 4.303A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 687 removed outlier: 3.661A pdb=" N LYS A 685 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.802A pdb=" N ASN A 747 " --> pdb=" O HIS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.604A pdb=" N LEU A 796 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 916 through 930 removed outlier: 6.987A pdb=" N ASN A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 972 through 974 No H-bonds generated for 'chain 'A' and resid 972 through 974' Processing helix chain 'A' and resid 983 through 990 removed outlier: 4.574A pdb=" N LYS A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1016 removed outlier: 3.734A pdb=" N HIS A1004 " --> pdb=" O TYR A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.764A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.926A pdb=" N ASP A1259 " --> pdb=" O PHE A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1266 Proline residue: A1263 - end of helix Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 3.725A pdb=" N TRP A1277 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1295 Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.581A pdb=" N LEU A1307 " --> pdb=" O GLY A1303 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A1310 " --> pdb=" O ASN A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1339 Processing helix chain 'A' and resid 1348 through 1357 removed outlier: 6.030A pdb=" N PHE A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N CYS A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A1356 " --> pdb=" O VAL A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1387 removed outlier: 3.577A pdb=" N LEU A1370 " --> pdb=" O ILE A1366 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A1380 " --> pdb=" O VAL A1376 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1393 removed outlier: 4.136A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1407 Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.778A pdb=" N ILE A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 3.572A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1508 Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1520 through 1525 removed outlier: 3.860A pdb=" N PHE A1523 " --> pdb=" O ARG A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1547 Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 4.219A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 Proline residue: A1643 - end of helix removed outlier: 4.009A pdb=" N ARG A1650 " --> pdb=" O GLN A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1662 Processing helix chain 'A' and resid 1701 through 1721 Processing helix chain 'C' and resid 189 through 210 removed outlier: 4.057A pdb=" N LEU C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 removed outlier: 4.591A pdb=" N PHE C 227 " --> pdb=" O HIS C 224 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'C' and resid 249 through 260 removed outlier: 3.512A pdb=" N LYS C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 311 removed outlier: 3.693A pdb=" N TYR C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 removed outlier: 3.890A pdb=" N ARG D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 46 through 50 removed outlier: 3.583A pdb=" N PHE D 49 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP D 50 " --> pdb=" O GLN D 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 50' Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 66 through 81 Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 116 through 125 Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 140 through 144 removed outlier: 3.530A pdb=" N HIS D 143 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 160 removed outlier: 3.687A pdb=" N THR D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 removed outlier: 3.522A pdb=" N LEU D 165 " --> pdb=" O GLN D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.871A pdb=" N LYS D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.975A pdb=" N MET D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 250 removed outlier: 4.301A pdb=" N ARG D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 292 Processing helix chain 'D' and resid 292 through 314 removed outlier: 3.946A pdb=" N ILE D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 302 " --> pdb=" O ILE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 343 Processing helix chain 'D' and resid 344 through 348 removed outlier: 3.635A pdb=" N ASP D 347 " --> pdb=" O MET D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 362 removed outlier: 3.916A pdb=" N ILE D 359 " --> pdb=" O THR D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 378 Processing helix chain 'D' and resid 382 through 386 removed outlier: 3.759A pdb=" N ILE D 386 " --> pdb=" O PRO D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 412 removed outlier: 3.517A pdb=" N CYS D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 399 " --> pdb=" O ARG D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 removed outlier: 4.332A pdb=" N VAL D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 510 through 535 Processing helix chain 'D' and resid 543 through 552 Processing helix chain 'D' and resid 567 through 569 No H-bonds generated for 'chain 'D' and resid 567 through 569' Processing helix chain 'D' and resid 570 through 582 removed outlier: 3.636A pdb=" N ILE D 582 " --> pdb=" O TYR D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 607 Processing helix chain 'D' and resid 608 through 611 Processing helix chain 'D' and resid 637 through 656 Processing helix chain 'D' and resid 667 through 680 removed outlier: 3.906A pdb=" N ILE D 675 " --> pdb=" O ARG D 671 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP D 677 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL D 678 " --> pdb=" O SER D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 687 removed outlier: 3.628A pdb=" N LYS D 685 " --> pdb=" O HIS D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 697 Processing helix chain 'D' and resid 741 through 748 removed outlier: 3.856A pdb=" N LEU D 746 " --> pdb=" O GLU D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 810 Processing helix chain 'D' and resid 845 through 852 Processing helix chain 'D' and resid 862 through 866 Processing helix chain 'D' and resid 873 through 878 removed outlier: 3.551A pdb=" N PHE D 877 " --> pdb=" O ARG D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 930 removed outlier: 7.520A pdb=" N ASN D 927 " --> pdb=" O SER D 923 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG D 928 " --> pdb=" O LYS D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 960 through 965 Processing helix chain 'D' and resid 972 through 976 Processing helix chain 'D' and resid 982 through 1017 Proline residue: D 993 - end of helix Processing helix chain 'D' and resid 1018 through 1025 Proline residue: D1022 - end of helix Processing helix chain 'D' and resid 1174 through 1182 Processing helix chain 'D' and resid 1183 through 1186 Processing helix chain 'D' and resid 1190 through 1199 Processing helix chain 'D' and resid 1209 through 1232 removed outlier: 4.071A pdb=" N LEU D1215 " --> pdb=" O ARG D1211 " (cutoff:3.500A) Processing helix chain 'D' and resid 1236 through 1248 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 3.766A pdb=" N ASP D1259 " --> pdb=" O PHE D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1262 through 1266 removed outlier: 3.587A pdb=" N LEU D1266 " --> pdb=" O PRO D1263 " (cutoff:3.500A) Processing helix chain 'D' and resid 1272 through 1277 removed outlier: 3.806A pdb=" N TRP D1277 " --> pdb=" O PRO D1273 " (cutoff:3.500A) Processing helix chain 'D' and resid 1285 through 1295 Processing helix chain 'D' and resid 1297 through 1302 removed outlier: 3.506A pdb=" N LYS D1300 " --> pdb=" O GLU D1297 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D1301 " --> pdb=" O PHE D1298 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D1302 " --> pdb=" O ALA D1299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1297 through 1302' Processing helix chain 'D' and resid 1303 through 1308 Processing helix chain 'D' and resid 1313 through 1319 Processing helix chain 'D' and resid 1324 through 1337 Processing helix chain 'D' and resid 1338 through 1341 removed outlier: 3.538A pdb=" N SER D1341 " --> pdb=" O ASN D1338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1338 through 1341' Processing helix chain 'D' and resid 1348 through 1351 removed outlier: 3.598A pdb=" N GLU D1351 " --> pdb=" O PHE D1348 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1348 through 1351' Processing helix chain 'D' and resid 1352 through 1357 removed outlier: 3.695A pdb=" N VAL D1356 " --> pdb=" O VAL D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1387 removed outlier: 8.005A pdb=" N LEU D1383 " --> pdb=" O LYS D1379 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N GLN D1384 " --> pdb=" O ASN D1380 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS D1385 " --> pdb=" O TYR D1381 " (cutoff:3.500A) Processing helix chain 'D' and resid 1387 through 1393 removed outlier: 4.117A pdb=" N GLU D1391 " --> pdb=" O PHE D1387 " (cutoff:3.500A) Processing helix chain 'D' and resid 1403 through 1407 Processing helix chain 'D' and resid 1422 through 1428 Processing helix chain 'D' and resid 1432 through 1441 Processing helix chain 'D' and resid 1446 through 1455 removed outlier: 4.392A pdb=" N LEU D1450 " --> pdb=" O ASP D1446 " (cutoff:3.500A) Processing helix chain 'D' and resid 1468 through 1491 removed outlier: 3.805A pdb=" N ILE D1474 " --> pdb=" O GLU D1470 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA D1477 " --> pdb=" O PHE D1473 " (cutoff:3.500A) Processing helix chain 'D' and resid 1495 through 1508 Processing helix chain 'D' and resid 1508 through 1519 Processing helix chain 'D' and resid 1521 through 1525 Processing helix chain 'D' and resid 1529 through 1546 Processing helix chain 'D' and resid 1609 through 1628 removed outlier: 4.340A pdb=" N GLY D1613 " --> pdb=" O PRO D1609 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D1616 " --> pdb=" O LEU D1612 " (cutoff:3.500A) Processing helix chain 'D' and resid 1629 through 1651 Proline residue: D1643 - end of helix Processing helix chain 'D' and resid 1655 through 1663 Processing helix chain 'D' and resid 1701 through 1721 Processing helix chain 'E' and resid 189 through 210 removed outlier: 3.913A pdb=" N ARG E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 removed outlier: 4.237A pdb=" N PHE E 227 " --> pdb=" O HIS E 224 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE E 230 " --> pdb=" O PHE E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 243 removed outlier: 3.997A pdb=" N GLU E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 261 Processing helix chain 'E' and resid 295 through 310 removed outlier: 4.620A pdb=" N TYR E 299 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 3.599A pdb=" N THR A 115 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARG A 59 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 136 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU A 61 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE A 138 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N MET A 63 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLY A 24 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR A 172 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A 26 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 25 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.259A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.540A pdb=" N ARG A 260 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.568A pdb=" N PHE A 558 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 771 Processing sheet with id=AA8, first strand: chain 'A' and resid 768 through 771 removed outlier: 4.793A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 753 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AB1, first strand: chain 'A' and resid 969 through 971 removed outlier: 4.082A pdb=" N VAL A 969 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 897 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 895 " --> pdb=" O LYS A 880 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS A 880 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1554 through 1558 removed outlier: 6.639A pdb=" N MET A1602 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A1603 " --> pdb=" O PHE A1698 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1554 through 1558 removed outlier: 6.639A pdb=" N MET A1602 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A1603 " --> pdb=" O PHE A1698 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 268 through 270 removed outlier: 4.247A pdb=" N LEU C 278 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 86 through 88 removed outlier: 3.549A pdb=" N VAL D 113 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 115 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA D 60 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLY D 114 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE D 62 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG D 59 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL D 135 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 61 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER D 134 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL D 169 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL D 136 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU D 171 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE D 138 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR D 172 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE D 25 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 219 through 225 removed outlier: 6.595A pdb=" N VAL D 476 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N PHE D 505 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE D 478 " --> pdb=" O PHE D 505 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N ALA D 507 " --> pdb=" O ILE D 478 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS D 388 " --> pdb=" O MET D 458 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N CYS D 460 " --> pdb=" O CYS D 388 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL D 390 " --> pdb=" O CYS D 460 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN D 422 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 260 through 261 removed outlier: 4.362A pdb=" N ARG D 260 " --> pdb=" O ARG D 269 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AB9, first strand: chain 'D' and resid 593 through 596 Processing sheet with id=AC1, first strand: chain 'D' and resid 703 through 706 Processing sheet with id=AC2, first strand: chain 'D' and resid 768 through 771 Processing sheet with id=AC3, first strand: chain 'D' and resid 768 through 771 removed outlier: 3.585A pdb=" N ILE D 729 " --> pdb=" O TYR D 754 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TYR D 754 " --> pdb=" O ILE D 729 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 830 " --> pdb=" O LEU D 757 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 819 through 820 Processing sheet with id=AC5, first strand: chain 'D' and resid 970 through 971 removed outlier: 3.794A pdb=" N LEU D 971 " --> pdb=" O ILE D 940 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARG D 943 " --> pdb=" O VAL D 895 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL D 895 " --> pdb=" O ARG D 943 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1554 through 1558 removed outlier: 7.347A pdb=" N MET D1602 " --> pdb=" O LEU D1557 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER D1603 " --> pdb=" O PHE D1698 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 1554 through 1558 removed outlier: 7.347A pdb=" N MET D1602 " --> pdb=" O LEU D1557 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER D1603 " --> pdb=" O PHE D1698 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 267 through 270 removed outlier: 4.311A pdb=" N LEU E 278 " --> pdb=" O VAL E 270 " (cutoff:3.500A) 1392 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 8.69 Time building geometry restraints manager: 3.43 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: 9107 1.34 - 1.46: 5382 1.46 - 1.58: 15411 1.58 - 1.70: 192 1.70 - 1.82: 242 Bond restraints: 30334 Sorted by residual: bond pdb=" CG1 ILE D1258 " pdb=" CD1 ILE D1258 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.56e+00 bond pdb=" CG LEU C 193 " pdb=" CD1 LEU C 193 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB GLU A1371 " pdb=" CG GLU A1371 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" C ILE D1262 " pdb=" N PRO D1263 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.33e+00 bond pdb=" CA MET A 967 " pdb=" CB MET A 967 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.21e-02 6.83e+03 1.26e+00 ... (remaining 30329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 40955 2.53 - 5.07: 496 5.07 - 7.60: 32 7.60 - 10.14: 3 10.14 - 12.67: 2 Bond angle restraints: 41488 Sorted by residual: angle pdb=" N GLY D 957 " pdb=" CA GLY D 957 " pdb=" C GLY D 957 " ideal model delta sigma weight residual 111.35 116.42 -5.07 1.20e+00 6.94e-01 1.79e+01 angle pdb=" CB MET A 620 " pdb=" CG MET A 620 " pdb=" SD MET A 620 " ideal model delta sigma weight residual 112.70 125.37 -12.67 3.00e+00 1.11e-01 1.78e+01 angle pdb=" CG ARG B 346 " pdb=" CD ARG B 346 " pdb=" NE ARG B 346 " ideal model delta sigma weight residual 112.00 119.73 -7.73 2.20e+00 2.07e-01 1.24e+01 angle pdb=" C3' C N 27 " pdb=" O3' C N 27 " pdb=" P A N 28 " ideal model delta sigma weight residual 119.70 123.69 -3.99 1.20e+00 6.94e-01 1.10e+01 angle pdb=" CA ALA C 286 " pdb=" C ALA C 286 " pdb=" N PHE C 287 " ideal model delta sigma weight residual 118.27 113.51 4.76 1.59e+00 3.96e-01 8.98e+00 ... (remaining 41483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.45: 17563 31.45 - 62.90: 563 62.90 - 94.34: 62 94.34 - 125.79: 0 125.79 - 157.24: 1 Dihedral angle restraints: 18189 sinusoidal: 8191 harmonic: 9998 Sorted by residual: dihedral pdb=" C4' U P 47 " pdb=" C3' U P 47 " pdb=" C2' U P 47 " pdb=" C1' U P 47 " ideal model delta sinusoidal sigma weight residual 36.34 -34.93 71.28 1 3.10e+00 1.04e-01 6.78e+02 dihedral pdb=" O4' U P 47 " pdb=" C4' U P 47 " pdb=" C3' U P 47 " pdb=" C2' U P 47 " ideal model delta sinusoidal sigma weight residual -35.15 24.45 -59.60 1 4.00e+00 6.25e-02 2.96e+02 dihedral pdb=" O4' U P 47 " pdb=" C2' U P 47 " pdb=" C1' U P 47 " pdb=" C3' U P 47 " ideal model delta sinusoidal sigma weight residual 25.59 -34.23 59.83 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 18186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3895 0.055 - 0.111: 674 0.111 - 0.166: 63 0.166 - 0.222: 15 0.222 - 0.277: 86 Chirality restraints: 4733 Sorted by residual: chirality pdb=" P A N 28 " pdb=" OP1 A N 28 " pdb=" OP2 A N 28 " pdb=" O5' A N 28 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2' U P 47 " pdb=" C3' U P 47 " pdb=" O2' U P 47 " pdb=" C1' U P 47 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" P C N 30 " pdb=" OP1 C N 30 " pdb=" OP2 C N 30 " pdb=" O5' C N 30 " both_signs ideal model delta sigma weight residual True 2.17 -2.44 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4730 not shown) Planarity restraints: 4953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 370 " 0.015 2.00e-02 2.50e+03 1.65e-02 4.76e+00 pdb=" CG PHE A 370 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 370 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 370 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 370 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 370 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 370 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 903 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO D 904 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO D 904 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 904 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 101 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C MET D 101 " -0.032 2.00e-02 2.50e+03 pdb=" O MET D 101 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP D 102 " 0.011 2.00e-02 2.50e+03 ... (remaining 4950 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 895 2.71 - 3.25: 31454 3.25 - 3.80: 49744 3.80 - 4.35: 63108 4.35 - 4.90: 99879 Nonbonded interactions: 245080 Sorted by model distance: nonbonded pdb=" OG SER D 264 " pdb=" OE1 GLN D 266 " model vdw 2.157 3.040 nonbonded pdb=" OG SER E 244 " pdb=" OE1 GLU E 246 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR D 182 " pdb=" OP1 A N 18 " model vdw 2.175 3.040 nonbonded pdb=" OD1 ASP A 944 " pdb=" N LEU A 945 " model vdw 2.188 3.120 nonbonded pdb=" O LEU A 341 " pdb=" OG1 THR A 345 " model vdw 2.195 3.040 ... (remaining 245075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'C' and resid 188 through 311) selection = chain 'E' } ncs_group { reference = (chain 'N' and resid 3 through 47) selection = (chain 'P' and resid 3 through 47) } 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.150 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 0.074 30334 Z= 0.127 Angle : 0.609 12.674 41488 Z= 0.307 Chirality : 0.052 0.277 4733 Planarity : 0.004 0.053 4953 Dihedral : 14.600 157.241 11701 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3370 helix: 0.87 (0.13), residues: 1591 sheet: -0.57 (0.26), residues: 363 loop : -0.18 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 604 TYR 0.014 0.001 TYR D1328 PHE 0.038 0.001 PHE A 370 TRP 0.022 0.002 TRP D 814 HIS 0.014 0.001 HIS C 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (30334) covalent geometry : angle 0.60932 / 0.31 (41488) hydrogen bonds : bond 0.17367 / 11.60 ( 1454) hydrogen bonds : angle 6.39253 / 4.50 ( 4120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.7060 (mm) cc_final: 0.6686 (mm) REVERT: A 317 LEU cc_start: 0.8314 (tp) cc_final: 0.7984 (tp) REVERT: A 494 ARG cc_start: 0.6537 (mmp-170) cc_final: 0.6140 (mmm160) REVERT: A 531 TYR cc_start: 0.8574 (t80) cc_final: 0.8354 (t80) REVERT: C 223 ARG cc_start: 0.7793 (ptt-90) cc_final: 0.7510 (ptt-90) REVERT: D 714 TYR cc_start: 0.8793 (t80) cc_final: 0.8513 (t80) REVERT: D 794 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8275 (pp20) REVERT: D 1209 MET cc_start: 0.7871 (mtm) cc_final: 0.7411 (mtm) REVERT: D 1333 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8916 (pt0) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.1660 time to fit residues: 82.8453 Evaluate side-chains 223 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS D 253 ASN D 747 ASN ** D 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1305 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.085933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.063135 restraints weight = 127595.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.065008 restraints weight = 71189.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.065359 restraints weight = 46018.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.065745 restraints weight = 38740.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.065789 restraints weight = 34945.508| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30334 Z= 0.181 Angle : 0.668 9.916 41488 Z= 0.330 Chirality : 0.046 0.396 4733 Planarity : 0.004 0.052 4953 Dihedral : 10.162 156.821 4846 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 0.95 % Allowed : 6.91 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3370 helix: 0.85 (0.13), residues: 1606 sheet: -0.73 (0.25), residues: 384 loop : -0.28 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 416 TYR 0.017 0.002 TYR A1468 PHE 0.019 0.002 PHE A1298 TRP 0.020 0.002 TRP D 814 HIS 0.007 0.001 HIS D1185 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (30334) covalent geometry : angle 0.66774 / 0.33 (41488) hydrogen bonds : bond 0.04968 / 3.35 ( 1454) hydrogen bonds : angle 4.95747 / 3.49 ( 4120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8138 (mmm) cc_final: 0.7770 (mmm) REVERT: A 531 TYR cc_start: 0.8723 (t80) cc_final: 0.8496 (t80) REVERT: A 589 PHE cc_start: 0.7695 (t80) cc_final: 0.7462 (t80) REVERT: A 620 MET cc_start: 0.8879 (mmm) cc_final: 0.8166 (mmm) REVERT: A 939 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6990 (mmp) REVERT: A 1417 MET cc_start: 0.1537 (tpt) cc_final: 0.1278 (tpt) REVERT: C 223 ARG cc_start: 0.8045 (ptt-90) cc_final: 0.7455 (ptt90) REVERT: D 154 MET cc_start: 0.8980 (mmm) cc_final: 0.8641 (mmm) REVERT: D 238 ILE cc_start: 0.9481 (mt) cc_final: 0.9261 (mp) REVERT: D 719 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.8244 (mtm-85) REVERT: D 747 ASN cc_start: 0.8400 (t0) cc_final: 0.8051 (t0) REVERT: D 794 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8302 (pp20) REVERT: D 992 LEU cc_start: 0.8421 (mm) cc_final: 0.8005 (mm) REVERT: D 1209 MET cc_start: 0.7920 (mtm) cc_final: 0.7370 (mtm) REVERT: D 1614 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8337 (t0) REVERT: D 1681 MET cc_start: 0.7647 (tmm) cc_final: 0.7364 (tmm) outliers start: 29 outliers final: 19 residues processed: 252 average time/residue: 0.1786 time to fit residues: 76.2881 Evaluate side-chains 238 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1355 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1614 ASP Chi-restraints excluded: chain D residue 1714 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 301 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 191 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 chunk 334 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 315 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN D 734 GLN D 778 HIS ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1656 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.085369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062574 restraints weight = 127793.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.063905 restraints weight = 76202.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.064585 restraints weight = 48394.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.064680 restraints weight = 48458.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.064758 restraints weight = 41600.521| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30334 Z= 0.188 Angle : 0.645 9.213 41488 Z= 0.319 Chirality : 0.045 0.397 4733 Planarity : 0.004 0.048 4953 Dihedral : 10.102 157.863 4846 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.20 % Rotamer: Outliers : 1.31 % Allowed : 10.03 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3370 helix: 0.79 (0.13), residues: 1609 sheet: -0.89 (0.25), residues: 382 loop : -0.42 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 719 TYR 0.018 0.002 TYR A1468 PHE 0.018 0.001 PHE A1001 TRP 0.019 0.002 TRP D 97 HIS 0.006 0.001 HIS D 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (30334) covalent geometry : angle 0.64525 / 0.32 (41488) hydrogen bonds : bond 0.04765 / 3.24 ( 1454) hydrogen bonds : angle 4.80801 / 3.40 ( 4120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8093 (mmm) cc_final: 0.7549 (mmm) REVERT: A 362 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.6084 (m-10) REVERT: A 531 TYR cc_start: 0.8666 (t80) cc_final: 0.8442 (t80) REVERT: A 589 PHE cc_start: 0.7623 (t80) cc_final: 0.7376 (t80) REVERT: A 829 TYR cc_start: 0.7811 (p90) cc_final: 0.6889 (p90) REVERT: A 939 MET cc_start: 0.7503 (tpp) cc_final: 0.7180 (mmp) REVERT: A 1209 MET cc_start: 0.7864 (ptt) cc_final: 0.7391 (ptt) REVERT: A 1371 GLU cc_start: 0.8145 (tt0) cc_final: 0.7932 (tt0) REVERT: C 218 MET cc_start: 0.8729 (ppp) cc_final: 0.8500 (ppp) REVERT: C 219 ARG cc_start: 0.8342 (tpt-90) cc_final: 0.7875 (tpt-90) REVERT: C 223 ARG cc_start: 0.7990 (ptt-90) cc_final: 0.7493 (ptt90) REVERT: D 208 MET cc_start: 0.7786 (mmm) cc_final: 0.7348 (mmp) REVERT: D 212 MET cc_start: 0.9108 (ppp) cc_final: 0.8891 (ppp) REVERT: D 344 MET cc_start: 0.7938 (ppp) cc_final: 0.7645 (ppp) REVERT: D 719 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8365 (mtm-85) REVERT: D 747 ASN cc_start: 0.8446 (t0) cc_final: 0.8174 (t0) REVERT: D 939 MET cc_start: 0.3893 (ppp) cc_final: 0.1811 (ptp) REVERT: D 992 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8129 (mm) REVERT: D 1209 MET cc_start: 0.7965 (mtm) cc_final: 0.7507 (mtm) REVERT: D 1614 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8277 (t0) REVERT: D 1681 MET cc_start: 0.7793 (tmm) cc_final: 0.7440 (tmm) REVERT: D 1689 MET cc_start: 0.7219 (tmm) cc_final: 0.6989 (mmm) outliers start: 40 outliers final: 27 residues processed: 251 average time/residue: 0.1850 time to fit residues: 78.0353 Evaluate side-chains 241 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1355 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1451 LEU Chi-restraints excluded: chain D residue 1614 ASP Chi-restraints excluded: chain D residue 1714 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 276 optimal weight: 0.5980 chunk 128 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 324 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 312 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 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 = 0.3881 r_free = 0.3881 target = 0.086736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.063666 restraints weight = 126370.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.065925 restraints weight = 69703.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.066352 restraints weight = 44115.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.066728 restraints weight = 34612.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.066805 restraints weight = 33791.158| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30334 Z= 0.119 Angle : 0.597 9.141 41488 Z= 0.290 Chirality : 0.043 0.336 4733 Planarity : 0.004 0.046 4953 Dihedral : 9.891 154.600 4846 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 1.51 % Allowed : 11.44 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3370 helix: 0.98 (0.13), residues: 1616 sheet: -0.81 (0.25), residues: 369 loop : -0.41 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 334 TYR 0.014 0.001 TYR E 231 PHE 0.015 0.001 PHE D 370 TRP 0.018 0.001 TRP A1634 HIS 0.006 0.001 HIS D1656 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (30334) covalent geometry : angle 0.59727 / 0.29 (41488) hydrogen bonds : bond 0.04149 / 2.83 ( 1454) hydrogen bonds : angle 4.56359 / 3.23 ( 4120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8047 (mmm) cc_final: 0.7527 (mmm) REVERT: A 362 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.6028 (m-10) REVERT: A 531 TYR cc_start: 0.8670 (t80) cc_final: 0.8459 (t80) REVERT: A 589 PHE cc_start: 0.7681 (t80) cc_final: 0.7388 (t80) REVERT: A 893 MET cc_start: 0.7947 (mpp) cc_final: 0.7640 (mpp) REVERT: A 907 TYR cc_start: 0.7976 (m-80) cc_final: 0.7674 (m-80) REVERT: A 1209 MET cc_start: 0.7718 (ptt) cc_final: 0.7316 (ptt) REVERT: C 219 ARG cc_start: 0.8333 (tpt-90) cc_final: 0.7767 (tpt-90) REVERT: C 225 ASN cc_start: 0.8622 (m-40) cc_final: 0.8403 (t0) REVERT: C 255 MET cc_start: 0.8798 (mpp) cc_final: 0.8595 (ptp) REVERT: C 266 LYS cc_start: 0.8624 (mppt) cc_final: 0.8270 (mppt) REVERT: D 208 MET cc_start: 0.7694 (mmm) cc_final: 0.7202 (mmp) REVERT: D 212 MET cc_start: 0.9039 (ppp) cc_final: 0.8808 (ppp) REVERT: D 344 MET cc_start: 0.7924 (ppp) cc_final: 0.7571 (ppp) REVERT: D 719 ARG cc_start: 0.8760 (mtm-85) cc_final: 0.8419 (mtm-85) REVERT: D 747 ASN cc_start: 0.8338 (t0) cc_final: 0.8021 (t0) REVERT: D 794 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8348 (pp20) REVERT: D 805 MET cc_start: 0.7666 (ppp) cc_final: 0.7070 (ppp) REVERT: D 893 MET cc_start: 0.7054 (pmm) cc_final: 0.6652 (pmm) REVERT: D 939 MET cc_start: 0.3884 (ppp) cc_final: 0.2293 (ptp) REVERT: D 992 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8096 (mm) REVERT: D 1002 LEU cc_start: 0.9041 (tt) cc_final: 0.8765 (tp) REVERT: D 1614 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8419 (t0) REVERT: D 1681 MET cc_start: 0.7919 (tmm) cc_final: 0.7558 (tmm) REVERT: D 1689 MET cc_start: 0.7406 (tmm) cc_final: 0.7001 (mmm) outliers start: 46 outliers final: 25 residues processed: 271 average time/residue: 0.1866 time to fit residues: 85.1435 Evaluate side-chains 246 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1451 LEU Chi-restraints excluded: chain D residue 1541 ASN Chi-restraints excluded: chain D residue 1614 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 156 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 263 optimal weight: 0.3980 chunk 302 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 275 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 339 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 122 optimal weight: 0.2980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1605 ASN ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.085859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.063089 restraints weight = 127690.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.064592 restraints weight = 78829.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.064840 restraints weight = 50220.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065175 restraints weight = 47788.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.065186 restraints weight = 42738.985| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30334 Z= 0.153 Angle : 0.611 9.499 41488 Z= 0.299 Chirality : 0.044 0.373 4733 Planarity : 0.004 0.048 4953 Dihedral : 9.838 156.381 4846 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 1.90 % Allowed : 12.29 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3370 helix: 0.97 (0.13), residues: 1623 sheet: -0.94 (0.25), residues: 375 loop : -0.46 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 334 TYR 0.021 0.001 TYR D1328 PHE 0.016 0.001 PHE D 370 TRP 0.016 0.001 TRP D 814 HIS 0.007 0.001 HIS D 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (30334) covalent geometry : angle 0.61067 / 0.30 (41488) hydrogen bonds : bond 0.04260 / 2.91 ( 1454) hydrogen bonds : angle 4.57021 / 3.23 ( 4120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8483 (tp) cc_final: 0.8091 (tt) REVERT: A 344 MET cc_start: 0.8099 (mmm) cc_final: 0.7598 (mmm) REVERT: A 362 PHE cc_start: 0.6515 (OUTLIER) cc_final: 0.6192 (m-10) REVERT: A 531 TYR cc_start: 0.8731 (t80) cc_final: 0.8518 (t80) REVERT: A 589 PHE cc_start: 0.7724 (t80) cc_final: 0.7440 (t80) REVERT: A 849 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7835 (ttm) REVERT: A 1209 MET cc_start: 0.7808 (ptt) cc_final: 0.7391 (ptt) REVERT: A 1343 TYR cc_start: 0.7873 (m-10) cc_final: 0.7189 (m-10) REVERT: C 218 MET cc_start: 0.8489 (ppp) cc_final: 0.8223 (ppp) REVERT: C 219 ARG cc_start: 0.8345 (tpt-90) cc_final: 0.7873 (tpt-90) REVERT: C 222 ASP cc_start: 0.8723 (m-30) cc_final: 0.8326 (m-30) REVERT: C 266 LYS cc_start: 0.8511 (mppt) cc_final: 0.8239 (mppt) REVERT: D 156 LEU cc_start: 0.9292 (tp) cc_final: 0.9069 (tp) REVERT: D 208 MET cc_start: 0.7845 (mmm) cc_final: 0.7294 (mmp) REVERT: D 344 MET cc_start: 0.8101 (ppp) cc_final: 0.7666 (ppp) REVERT: D 719 ARG cc_start: 0.8693 (mtm-85) cc_final: 0.8252 (mtm-85) REVERT: D 747 ASN cc_start: 0.8329 (t0) cc_final: 0.7986 (t0) REVERT: D 779 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8803 (p) REVERT: D 794 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8265 (pp20) REVERT: D 805 MET cc_start: 0.7581 (ppp) cc_final: 0.7005 (ppp) REVERT: D 992 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8102 (mm) REVERT: D 995 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9018 (tp) REVERT: D 1002 LEU cc_start: 0.9032 (tt) cc_final: 0.8796 (tp) REVERT: D 1328 TYR cc_start: 0.5983 (OUTLIER) cc_final: 0.5595 (t80) REVERT: D 1614 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8420 (t0) REVERT: D 1681 MET cc_start: 0.7820 (tmm) cc_final: 0.7518 (tmm) REVERT: D 1689 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7002 (mmm) outliers start: 58 outliers final: 39 residues processed: 256 average time/residue: 0.1777 time to fit residues: 77.3431 Evaluate side-chains 256 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1355 CYS Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 995 ILE Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1451 LEU Chi-restraints excluded: chain D residue 1541 ASN Chi-restraints excluded: chain D residue 1614 ASP Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1714 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 82 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 chunk 167 optimal weight: 0.1980 chunk 86 optimal weight: 0.0970 chunk 209 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 257 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 chunk 283 optimal weight: 0.0040 chunk 271 optimal weight: 9.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 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 = 0.3902 r_free = 0.3902 target = 0.087693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.064757 restraints weight = 127123.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.066983 restraints weight = 67412.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.067413 restraints weight = 44540.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.067729 restraints weight = 34657.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.067864 restraints weight = 33146.720| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 30334 Z= 0.104 Angle : 0.594 13.534 41488 Z= 0.286 Chirality : 0.043 0.308 4733 Planarity : 0.003 0.052 4953 Dihedral : 9.681 153.642 4846 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.70 % Allowed : 13.07 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3370 helix: 1.05 (0.13), residues: 1631 sheet: -0.78 (0.26), residues: 364 loop : -0.38 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 334 TYR 0.021 0.001 TYR D1328 PHE 0.017 0.001 PHE A 370 TRP 0.018 0.001 TRP A1634 HIS 0.008 0.001 HIS D 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (30334) covalent geometry : angle 0.59389 / 0.29 (41488) hydrogen bonds : bond 0.03887 / 2.65 ( 1454) hydrogen bonds : angle 4.41791 / 3.12 ( 4120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.8956 (ttp) cc_final: 0.8651 (ttp) REVERT: A 344 MET cc_start: 0.8117 (mmm) cc_final: 0.7578 (mmm) REVERT: A 362 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.6025 (m-10) REVERT: A 372 MET cc_start: 0.8017 (mpp) cc_final: 0.7606 (mpp) REVERT: A 589 PHE cc_start: 0.7636 (t80) cc_final: 0.7341 (t80) REVERT: A 893 MET cc_start: 0.7846 (mpp) cc_final: 0.7611 (mpp) REVERT: A 1209 MET cc_start: 0.7696 (ptt) cc_final: 0.7222 (ptt) REVERT: A 1343 TYR cc_start: 0.7722 (m-10) cc_final: 0.7111 (m-10) REVERT: C 223 ARG cc_start: 0.7874 (ptt-90) cc_final: 0.7310 (tmm-80) REVERT: C 266 LYS cc_start: 0.8546 (mppt) cc_final: 0.8256 (mppt) REVERT: D 156 LEU cc_start: 0.9176 (tp) cc_final: 0.8949 (tp) REVERT: D 208 MET cc_start: 0.7755 (mmm) cc_final: 0.7222 (mmp) REVERT: D 344 MET cc_start: 0.7960 (ppp) cc_final: 0.7538 (ppp) REVERT: D 625 MET cc_start: 0.8359 (tpp) cc_final: 0.8156 (mmm) REVERT: D 747 ASN cc_start: 0.8350 (t0) cc_final: 0.8008 (t0) REVERT: D 779 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8770 (p) REVERT: D 794 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8319 (pp20) REVERT: D 805 MET cc_start: 0.7553 (ppp) cc_final: 0.7003 (ppp) REVERT: D 992 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7874 (mm) REVERT: D 1002 LEU cc_start: 0.8963 (tt) cc_final: 0.8719 (tp) REVERT: D 1328 TYR cc_start: 0.6097 (OUTLIER) cc_final: 0.5674 (t80) REVERT: D 1614 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8376 (t0) REVERT: D 1681 MET cc_start: 0.7882 (tmm) cc_final: 0.7585 (tmm) REVERT: D 1689 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7077 (mmm) REVERT: E 256 ASP cc_start: 0.7908 (t0) cc_final: 0.7630 (t0) outliers start: 52 outliers final: 32 residues processed: 272 average time/residue: 0.1800 time to fit residues: 83.2913 Evaluate side-chains 259 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1310 LEU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain D residue 1451 LEU Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1514 CYS Chi-restraints excluded: chain D residue 1541 ASN Chi-restraints excluded: chain D residue 1614 ASP Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 39 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 258 optimal weight: 20.0000 chunk 289 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 ASN B 349 GLN ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.086517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063643 restraints weight = 127918.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.065633 restraints weight = 71138.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066039 restraints weight = 49116.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.066483 restraints weight = 38103.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.066592 restraints weight = 34612.811| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30334 Z= 0.135 Angle : 0.606 15.611 41488 Z= 0.292 Chirality : 0.043 0.360 4733 Planarity : 0.004 0.052 4953 Dihedral : 9.662 155.414 4846 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 2.03 % Allowed : 13.76 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3370 helix: 1.11 (0.13), residues: 1621 sheet: -0.83 (0.25), residues: 375 loop : -0.35 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.023 0.001 TYR A 531 PHE 0.014 0.001 PHE D 370 TRP 0.020 0.001 TRP D 986 HIS 0.008 0.001 HIS C 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (30334) covalent geometry : angle 0.60630 / 0.29 (41488) hydrogen bonds : bond 0.04017 / 2.74 ( 1454) hydrogen bonds : angle 4.43129 / 3.14 ( 4120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 223 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.5675 (mt0) cc_final: 0.5467 (mm-40) REVERT: A 322 MET cc_start: 0.9053 (ttp) cc_final: 0.8679 (ttp) REVERT: A 344 MET cc_start: 0.8114 (mmm) cc_final: 0.7582 (mmm) REVERT: A 360 MET cc_start: 0.7907 (tpt) cc_final: 0.7497 (mmt) REVERT: A 362 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.6132 (m-10) REVERT: A 372 MET cc_start: 0.8071 (mpp) cc_final: 0.7613 (mpp) REVERT: A 589 PHE cc_start: 0.7632 (t80) cc_final: 0.7353 (t80) REVERT: A 805 MET cc_start: 0.8881 (tmm) cc_final: 0.8218 (tmm) REVERT: A 893 MET cc_start: 0.7925 (mpp) cc_final: 0.7619 (mpp) REVERT: A 939 MET cc_start: 0.7374 (tpp) cc_final: 0.6816 (mmp) REVERT: A 1209 MET cc_start: 0.7799 (ptt) cc_final: 0.7346 (ptt) REVERT: A 1343 TYR cc_start: 0.7666 (m-80) cc_final: 0.7065 (m-10) REVERT: C 218 MET cc_start: 0.8399 (ppp) cc_final: 0.8190 (ppp) REVERT: C 219 ARG cc_start: 0.8345 (tpt-90) cc_final: 0.8026 (tpp80) REVERT: C 223 ARG cc_start: 0.7631 (ptt-90) cc_final: 0.7352 (ptt90) REVERT: D 156 LEU cc_start: 0.9202 (tp) cc_final: 0.8958 (tp) REVERT: D 208 MET cc_start: 0.7853 (mmm) cc_final: 0.7330 (mmp) REVERT: D 344 MET cc_start: 0.8019 (ppp) cc_final: 0.7602 (ppp) REVERT: D 458 MET cc_start: 0.8296 (tpt) cc_final: 0.7947 (tpt) REVERT: D 794 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8301 (pp20) REVERT: D 805 MET cc_start: 0.7524 (ppp) cc_final: 0.6954 (ppp) REVERT: D 939 MET cc_start: 0.4512 (ppp) cc_final: 0.2050 (mmt) REVERT: D 992 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7921 (mm) REVERT: D 1002 LEU cc_start: 0.8966 (tt) cc_final: 0.8750 (tp) REVERT: D 1328 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.5729 (t80) REVERT: D 1614 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8313 (t0) REVERT: D 1681 MET cc_start: 0.7949 (tmm) cc_final: 0.7625 (tmm) REVERT: D 1689 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6920 (mmm) outliers start: 62 outliers final: 47 residues processed: 265 average time/residue: 0.1712 time to fit residues: 77.1658 Evaluate side-chains 266 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1185 HIS Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1310 LEU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1348 PHE Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain D residue 1451 LEU Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1514 CYS Chi-restraints excluded: chain D residue 1541 ASN Chi-restraints excluded: chain D residue 1614 ASP Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1714 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 148 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 323 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 chunk 319 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS ** D1191 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 = 0.3892 r_free = 0.3892 target = 0.087172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064186 restraints weight = 128107.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.066352 restraints weight = 70817.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.066644 restraints weight = 48909.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.067212 restraints weight = 37447.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.067220 restraints weight = 34442.121| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30334 Z= 0.115 Angle : 0.602 16.196 41488 Z= 0.288 Chirality : 0.043 0.334 4733 Planarity : 0.003 0.055 4953 Dihedral : 9.593 154.444 4846 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 1.93 % Allowed : 14.02 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 3370 helix: 1.11 (0.13), residues: 1630 sheet: -0.79 (0.25), residues: 371 loop : -0.34 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 334 TYR 0.022 0.001 TYR A 531 PHE 0.015 0.001 PHE D 981 TRP 0.017 0.001 TRP D 986 HIS 0.006 0.001 HIS C 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (30334) covalent geometry : angle 0.60192 / 0.29 (41488) hydrogen bonds : bond 0.03880 / 2.66 ( 1454) hydrogen bonds : angle 4.36639 / 3.09 ( 4120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 225 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.5829 (mt0) cc_final: 0.5596 (mm-40) REVERT: A 322 MET cc_start: 0.9019 (ttp) cc_final: 0.8680 (ttp) REVERT: A 344 MET cc_start: 0.8140 (mmm) cc_final: 0.7603 (mmm) REVERT: A 360 MET cc_start: 0.7886 (tpt) cc_final: 0.7269 (mtm) REVERT: A 362 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.6183 (m-10) REVERT: A 372 MET cc_start: 0.8028 (mpp) cc_final: 0.7620 (mpp) REVERT: A 805 MET cc_start: 0.8896 (tmm) cc_final: 0.8273 (tmm) REVERT: A 893 MET cc_start: 0.7829 (mpp) cc_final: 0.7520 (mpp) REVERT: A 939 MET cc_start: 0.7237 (tpp) cc_final: 0.6999 (mmp) REVERT: A 1209 MET cc_start: 0.7790 (ptt) cc_final: 0.7326 (ptt) REVERT: A 1343 TYR cc_start: 0.7697 (m-80) cc_final: 0.7089 (m-10) REVERT: A 1371 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: C 218 MET cc_start: 0.8294 (ppp) cc_final: 0.7943 (ppp) REVERT: C 219 ARG cc_start: 0.8301 (tpt-90) cc_final: 0.7921 (tpp80) REVERT: C 223 ARG cc_start: 0.7740 (ptt-90) cc_final: 0.7316 (ptt90) REVERT: C 309 MET cc_start: 0.7765 (mmm) cc_final: 0.7461 (mmm) REVERT: D 156 LEU cc_start: 0.9166 (tp) cc_final: 0.8921 (tp) REVERT: D 208 MET cc_start: 0.7830 (mmm) cc_final: 0.7333 (mmp) REVERT: D 344 MET cc_start: 0.7901 (ppp) cc_final: 0.7484 (ppp) REVERT: D 747 ASN cc_start: 0.8181 (p0) cc_final: 0.7943 (p0) REVERT: D 794 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8327 (pp20) REVERT: D 805 MET cc_start: 0.7477 (ppp) cc_final: 0.6921 (ppp) REVERT: D 852 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6326 (m-10) REVERT: D 939 MET cc_start: 0.4539 (ppp) cc_final: 0.2058 (mmt) REVERT: D 992 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7878 (mm) REVERT: D 1002 LEU cc_start: 0.9001 (tt) cc_final: 0.8799 (tp) REVERT: D 1003 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7475 (mm) REVERT: D 1328 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.5735 (t80) REVERT: D 1614 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8352 (t0) REVERT: D 1681 MET cc_start: 0.7930 (tmm) cc_final: 0.7614 (tmm) REVERT: D 1689 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6954 (mmm) REVERT: E 246 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: E 256 ASP cc_start: 0.7933 (t0) cc_final: 0.7665 (t0) outliers start: 59 outliers final: 44 residues processed: 265 average time/residue: 0.1558 time to fit residues: 70.6109 Evaluate side-chains 273 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1371 GLU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 852 PHE Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1310 LEU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain D residue 1451 LEU Chi-restraints excluded: chain D residue 1474 ILE Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1514 CYS Chi-restraints excluded: chain D residue 1541 ASN Chi-restraints excluded: chain D residue 1614 ASP Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1714 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 320 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 219 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 249 optimal weight: 0.9990 chunk 220 optimal weight: 0.9990 chunk 279 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 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 = 0.3892 r_free = 0.3892 target = 0.087197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064142 restraints weight = 127550.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.066292 restraints weight = 74269.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.066524 restraints weight = 45933.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.066866 restraints weight = 39601.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.066962 restraints weight = 36132.206| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30334 Z= 0.115 Angle : 0.610 16.442 41488 Z= 0.290 Chirality : 0.043 0.339 4733 Planarity : 0.003 0.055 4953 Dihedral : 9.532 154.421 4846 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 2.16 % Allowed : 13.89 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3370 helix: 1.15 (0.13), residues: 1630 sheet: -0.77 (0.26), residues: 371 loop : -0.31 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 998 TYR 0.034 0.001 TYR A 521 PHE 0.016 0.001 PHE A 153 TRP 0.016 0.001 TRP A1634 HIS 0.006 0.001 HIS C 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (30334) covalent geometry : angle 0.60955 / 0.29 (41488) hydrogen bonds : bond 0.03849 / 2.64 ( 1454) hydrogen bonds : angle 4.33951 / 3.07 ( 4120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.5914 (mt0) cc_final: 0.5674 (mm-40) REVERT: A 317 LEU cc_start: 0.8061 (tt) cc_final: 0.7769 (tp) REVERT: A 322 MET cc_start: 0.9037 (ttp) cc_final: 0.8649 (ttp) REVERT: A 344 MET cc_start: 0.8154 (mmm) cc_final: 0.7606 (mmm) REVERT: A 360 MET cc_start: 0.7793 (tpt) cc_final: 0.7401 (mtm) REVERT: A 362 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.6173 (m-10) REVERT: A 805 MET cc_start: 0.8914 (tmm) cc_final: 0.8347 (tmm) REVERT: A 893 MET cc_start: 0.7904 (mpp) cc_final: 0.7575 (mpp) REVERT: A 939 MET cc_start: 0.7303 (tpp) cc_final: 0.7095 (mmp) REVERT: A 1209 MET cc_start: 0.7823 (ptt) cc_final: 0.7356 (ptt) REVERT: A 1343 TYR cc_start: 0.7702 (m-80) cc_final: 0.7079 (m-10) REVERT: C 218 MET cc_start: 0.8357 (ppp) cc_final: 0.8042 (ppp) REVERT: C 219 ARG cc_start: 0.8319 (tpt-90) cc_final: 0.7931 (tpp80) REVERT: C 223 ARG cc_start: 0.7729 (ptt-90) cc_final: 0.7296 (ptt90) REVERT: D 156 LEU cc_start: 0.9164 (tp) cc_final: 0.8924 (tp) REVERT: D 208 MET cc_start: 0.7868 (mmm) cc_final: 0.7359 (mmp) REVERT: D 344 MET cc_start: 0.7993 (ppp) cc_final: 0.7563 (ppp) REVERT: D 747 ASN cc_start: 0.8095 (p0) cc_final: 0.7807 (p0) REVERT: D 794 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8360 (pp20) REVERT: D 805 MET cc_start: 0.7435 (ppp) cc_final: 0.6897 (ppp) REVERT: D 852 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.6232 (m-10) REVERT: D 939 MET cc_start: 0.4555 (ppp) cc_final: 0.2971 (ptp) REVERT: D 992 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7887 (mm) REVERT: D 1003 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7487 (mm) REVERT: D 1328 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.5662 (t80) REVERT: D 1614 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8327 (t0) REVERT: D 1681 MET cc_start: 0.7938 (tmm) cc_final: 0.7578 (tmm) REVERT: D 1689 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6966 (mmm) REVERT: E 246 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7175 (pm20) REVERT: E 256 ASP cc_start: 0.7987 (t0) cc_final: 0.7731 (t0) outliers start: 66 outliers final: 53 residues processed: 267 average time/residue: 0.1497 time to fit residues: 68.7514 Evaluate side-chains 280 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 219 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 852 PHE Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 934 HIS Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1310 LEU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1348 PHE Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain D residue 1451 LEU Chi-restraints excluded: chain D residue 1474 ILE Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1541 ASN Chi-restraints excluded: chain D residue 1606 VAL Chi-restraints excluded: chain D residue 1614 ASP Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1714 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 198 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 54 optimal weight: 30.0000 chunk 95 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 240 optimal weight: 0.4980 chunk 18 optimal weight: 0.0170 chunk 63 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 145 optimal weight: 0.0980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1433 HIS D 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.088158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065274 restraints weight = 127458.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.067671 restraints weight = 70861.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.067953 restraints weight = 44922.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.068377 restraints weight = 36604.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.068453 restraints weight = 34250.584| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 30334 Z= 0.103 Angle : 0.619 16.574 41488 Z= 0.291 Chirality : 0.043 0.309 4733 Planarity : 0.003 0.054 4953 Dihedral : 9.445 153.196 4846 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 1.74 % Allowed : 14.61 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 3370 helix: 1.18 (0.13), residues: 1634 sheet: -0.63 (0.26), residues: 365 loop : -0.26 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 998 TYR 0.021 0.001 TYR A 521 PHE 0.016 0.001 PHE A 153 TRP 0.020 0.001 TRP A1634 HIS 0.007 0.001 HIS D 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (30334) covalent geometry : angle 0.61915 / 0.29 (41488) hydrogen bonds : bond 0.03752 / 2.57 ( 1454) hydrogen bonds : angle 4.28685 / 3.03 ( 4120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 233 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.8978 (ttp) cc_final: 0.8664 (ttp) REVERT: A 344 MET cc_start: 0.8142 (mmm) cc_final: 0.7579 (mmm) REVERT: A 362 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.6043 (m-10) REVERT: A 805 MET cc_start: 0.8809 (tmm) cc_final: 0.8378 (tmm) REVERT: A 893 MET cc_start: 0.7810 (mpp) cc_final: 0.7459 (mpp) REVERT: A 1209 MET cc_start: 0.7630 (ptt) cc_final: 0.7164 (ptt) REVERT: A 1343 TYR cc_start: 0.7547 (m-80) cc_final: 0.6884 (m-10) REVERT: C 218 MET cc_start: 0.8299 (ppp) cc_final: 0.7933 (ppp) REVERT: C 219 ARG cc_start: 0.8260 (tpt-90) cc_final: 0.7863 (tpp80) REVERT: C 223 ARG cc_start: 0.7671 (ptt-90) cc_final: 0.7217 (ptt90) REVERT: D 156 LEU cc_start: 0.9134 (tp) cc_final: 0.8889 (tp) REVERT: D 208 MET cc_start: 0.7877 (mmm) cc_final: 0.7393 (mmp) REVERT: D 344 MET cc_start: 0.7906 (ppp) cc_final: 0.7526 (ppp) REVERT: D 458 MET cc_start: 0.8306 (tpt) cc_final: 0.8028 (tpt) REVERT: D 747 ASN cc_start: 0.8066 (p0) cc_final: 0.7719 (p0) REVERT: D 794 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8349 (pp20) REVERT: D 852 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.6384 (m-10) REVERT: D 939 MET cc_start: 0.4573 (ppp) cc_final: 0.3031 (ptp) REVERT: D 992 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7824 (mm) REVERT: D 1209 MET cc_start: 0.7703 (mtm) cc_final: 0.7453 (mtm) REVERT: D 1328 TYR cc_start: 0.6513 (OUTLIER) cc_final: 0.5773 (t80) REVERT: D 1681 MET cc_start: 0.7939 (tmm) cc_final: 0.7588 (tmm) REVERT: D 1689 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6965 (mmm) REVERT: E 246 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: E 256 ASP cc_start: 0.7937 (t0) cc_final: 0.7705 (t0) outliers start: 53 outliers final: 38 residues processed: 268 average time/residue: 0.1691 time to fit residues: 77.4498 Evaluate side-chains 266 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 852 PHE Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 934 HIS Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1292 TRP Chi-restraints excluded: chain D residue 1310 LEU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain D residue 1451 LEU Chi-restraints excluded: chain D residue 1474 ILE Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1594 VAL Chi-restraints excluded: chain D residue 1606 VAL Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1714 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 311 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 296 optimal weight: 0.5980 chunk 278 optimal weight: 5.9990 chunk 336 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 884 GLN ** C 224 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 = 0.3893 r_free = 0.3893 target = 0.087226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.064371 restraints weight = 126577.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066299 restraints weight = 73195.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.066751 restraints weight = 44510.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.066903 restraints weight = 39434.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.067102 restraints weight = 36685.324| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30334 Z= 0.124 Angle : 0.621 13.724 41488 Z= 0.296 Chirality : 0.043 0.347 4733 Planarity : 0.004 0.054 4953 Dihedral : 9.452 154.108 4846 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 1.77 % Allowed : 14.68 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 3370 helix: 1.17 (0.13), residues: 1637 sheet: -0.61 (0.26), residues: 366 loop : -0.26 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 334 TYR 0.044 0.001 TYR A 519 PHE 0.019 0.001 PHE A 153 TRP 0.014 0.001 TRP A1634 HIS 0.006 0.001 HIS D 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (30334) covalent geometry : angle 0.62078 / 0.30 (41488) hydrogen bonds : bond 0.03847 / 2.65 ( 1454) hydrogen bonds : angle 4.33059 / 3.05 ( 4120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4764.75 seconds wall clock time: 83 minutes 44.12 seconds (5024.12 seconds total)