Starting phenix.real_space_refine on Wed Jun 25 20:20:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hf0_34707/06_2025/8hf0_34707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf0_34707/06_2025/8hf0_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_34707/06_2025/8hf0_34707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf0_34707/06_2025/8hf0_34707.map" model { file = "/net/cci-nas-00/data/ceres_data/8hf0_34707/06_2025/8hf0_34707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf0_34707/06_2025/8hf0_34707.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'RNA': 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: {'RNA': 50} Modifications used: {'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna3p': 49} Time building chain proxies: 15.49, per 1000 atoms: 0.52 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: 6.89 Conformation dependent library (CDL) restraints added in 3.4 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: 10.82 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: 17.63 Time building geometry restraints manager: 8.27 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: 41117 2.53 - 5.07: 335 5.07 - 7.60: 31 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=" 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 angle pdb=" N ILE D 582 " pdb=" CA ILE D 582 " pdb=" C ILE D 582 " ideal model delta sigma weight residual 108.88 115.26 -6.38 2.16e+00 2.14e-01 8.72e+00 ... (remaining 41483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.45: 17791 31.45 - 62.90: 596 62.90 - 94.34: 146 94.34 - 125.79: 1 125.79 - 157.24: 1 Dihedral angle restraints: 18535 sinusoidal: 8537 harmonic: 9998 Sorted by residual: dihedral pdb=" CA CYS C 285 " pdb=" C CYS C 285 " pdb=" N ALA C 286 " pdb=" CA ALA C 286 " ideal model delta harmonic sigma weight residual 180.00 154.67 25.33 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA MET D 101 " pdb=" C MET D 101 " pdb=" N TRP D 102 " pdb=" CA TRP D 102 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ARG A 427 " pdb=" C ARG A 427 " pdb=" N ASN A 428 " pdb=" CA ASN A 428 " ideal model delta harmonic sigma weight residual 180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 18532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3260 0.035 - 0.070: 1026 0.070 - 0.105: 342 0.105 - 0.140: 97 0.140 - 0.175: 8 Chirality restraints: 4733 Sorted by residual: chirality pdb=" C3' C N 27 " pdb=" C4' C N 27 " pdb=" O3' C N 27 " pdb=" C2' C N 27 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA ILE A1654 " pdb=" N ILE A1654 " pdb=" C ILE A1654 " pdb=" CB ILE A1654 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CG LEU D 992 " pdb=" CB LEU D 992 " pdb=" CD1 LEU D 992 " pdb=" CD2 LEU D 992 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.56e-01 ... (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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 74.990 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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= 0.125 Angle : 0.574 12.674 41488 Z= 0.300 Chirality : 0.040 0.175 4733 Planarity : 0.004 0.053 4953 Dihedral : 15.853 157.241 12047 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.022 0.002 TRP D 814 HIS 0.014 0.001 HIS C 224 PHE 0.038 0.001 PHE A 370 TYR 0.014 0.001 TYR D1328 ARG 0.007 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.17367 ( 1454) hydrogen bonds : angle 6.39253 ( 4120) covalent geometry : bond 0.00276 (30334) covalent geometry : angle 0.57397 (41488) *********************** 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 : 2.993 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: 0.7983 (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: 0.3821 time to fit residues: 189.0447 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 : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 314 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3876 r_free = 0.3876 target = 0.086407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.063779 restraints weight = 127186.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.065638 restraints weight = 73968.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.065913 restraints weight = 48378.741| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30334 Z= 0.156 Angle : 0.612 10.704 41488 Z= 0.316 Chirality : 0.042 0.304 4733 Planarity : 0.004 0.051 4953 Dihedral : 14.184 160.704 5192 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 0.92 % Allowed : 6.75 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3370 helix: 0.88 (0.13), residues: 1609 sheet: -0.63 (0.26), residues: 374 loop : -0.28 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 814 HIS 0.006 0.001 HIS D1185 PHE 0.018 0.001 PHE A1001 TYR 0.016 0.001 TYR A1468 ARG 0.005 0.001 ARG D 719 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 1454) hydrogen bonds : angle 4.90399 ( 4120) covalent geometry : bond 0.00348 (30334) covalent geometry : angle 0.61228 (41488) *********************** 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 273 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8293 (mpp80) REVERT: A 344 MET cc_start: 0.8125 (mmm) cc_final: 0.7631 (mmm) REVERT: A 531 TYR cc_start: 0.8696 (t80) cc_final: 0.8474 (t80) REVERT: A 589 PHE cc_start: 0.7770 (t80) cc_final: 0.7538 (t80) REVERT: A 620 MET cc_start: 0.8856 (mmm) cc_final: 0.8147 (mmm) REVERT: A 939 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6966 (mmp) REVERT: A 1417 MET cc_start: 0.1450 (tpt) cc_final: 0.1172 (tpt) REVERT: D 154 MET cc_start: 0.8892 (mmm) cc_final: 0.8546 (mmm) REVERT: D 156 LEU cc_start: 0.9307 (tp) cc_final: 0.9082 (tp) REVERT: D 238 ILE cc_start: 0.9474 (mt) cc_final: 0.9267 (mp) REVERT: D 714 TYR cc_start: 0.8819 (t80) cc_final: 0.8532 (t80) REVERT: D 719 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8253 (mtm-85) REVERT: D 747 ASN cc_start: 0.8403 (t0) cc_final: 0.8051 (t0) REVERT: D 794 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8300 (pp20) REVERT: D 992 LEU cc_start: 0.8394 (mm) cc_final: 0.8050 (mm) REVERT: D 1209 MET cc_start: 0.7924 (mtm) cc_final: 0.7381 (mtm) REVERT: D 1614 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8310 (t0) REVERT: D 1681 MET cc_start: 0.7649 (tmm) cc_final: 0.7403 (tmm) REVERT: D 1689 MET cc_start: 0.7242 (tmm) cc_final: 0.7030 (mmm) outliers start: 28 outliers final: 17 residues processed: 259 average time/residue: 0.3846 time to fit residues: 167.2414 Evaluate side-chains 239 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 236 ARG 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 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 45 optimal weight: 20.0000 chunk 279 optimal weight: 10.0000 chunk 278 optimal weight: 0.7980 chunk 255 optimal weight: 30.0000 chunk 280 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 304 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 326 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** 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** D 287 GLN D 734 GLN D 778 HIS D1191 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.085716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.062736 restraints weight = 126281.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.064882 restraints weight = 69638.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065073 restraints weight = 43205.532| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 30334 Z= 0.169 Angle : 0.589 9.064 41488 Z= 0.304 Chirality : 0.041 0.203 4733 Planarity : 0.004 0.047 4953 Dihedral : 14.197 161.129 5192 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 1.34 % Allowed : 9.73 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3370 helix: 0.87 (0.13), residues: 1610 sheet: -0.82 (0.25), residues: 377 loop : -0.38 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 814 HIS 0.008 0.001 HIS C 224 PHE 0.018 0.001 PHE A1001 TYR 0.016 0.001 TYR A1468 ARG 0.005 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 1454) hydrogen bonds : angle 4.74631 ( 4120) covalent geometry : bond 0.00381 (30334) covalent geometry : angle 0.58929 (41488) *********************** 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 267 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8100 (mmm) cc_final: 0.7551 (mmm) REVERT: A 362 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.6035 (m-10) REVERT: A 531 TYR cc_start: 0.8705 (t80) cc_final: 0.8472 (t80) REVERT: A 589 PHE cc_start: 0.7777 (t80) cc_final: 0.7513 (t80) REVERT: A 829 TYR cc_start: 0.7848 (p90) cc_final: 0.6878 (p90) REVERT: A 849 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8049 (mtp) REVERT: A 922 MET cc_start: 0.8549 (mmm) cc_final: 0.8343 (mmm) REVERT: A 939 MET cc_start: 0.7522 (tpp) cc_final: 0.7206 (mmp) REVERT: A 1209 MET cc_start: 0.7808 (ptt) cc_final: 0.7344 (ptt) REVERT: A 1371 GLU cc_start: 0.8182 (tt0) cc_final: 0.7927 (tt0) REVERT: C 218 MET cc_start: 0.8691 (ppp) cc_final: 0.8468 (ppp) REVERT: C 219 ARG cc_start: 0.8326 (tpt-90) cc_final: 0.7831 (tpt-90) REVERT: D 208 MET cc_start: 0.7738 (mmm) cc_final: 0.7298 (mmp) REVERT: D 212 MET cc_start: 0.9083 (ppp) cc_final: 0.8860 (ppp) REVERT: D 344 MET cc_start: 0.7938 (ppp) cc_final: 0.7635 (ppp) REVERT: D 719 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8355 (mpp80) REVERT: D 747 ASN cc_start: 0.8413 (t0) cc_final: 0.8141 (t0) REVERT: D 794 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8307 (pp20) REVERT: D 805 MET cc_start: 0.7608 (ppp) cc_final: 0.6978 (ppp) REVERT: D 939 MET cc_start: 0.3811 (ppp) cc_final: 0.1925 (ptp) REVERT: D 992 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8103 (mm) REVERT: D 1016 LEU cc_start: 0.7755 (mm) cc_final: 0.7459 (mt) REVERT: D 1029 MET cc_start: 0.8112 (mmm) cc_final: 0.7900 (mmm) REVERT: D 1614 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8402 (t0) REVERT: D 1681 MET cc_start: 0.7730 (tmm) cc_final: 0.7376 (tmm) REVERT: D 1689 MET cc_start: 0.7286 (tmm) cc_final: 0.7048 (mmm) outliers start: 41 outliers final: 28 residues processed: 251 average time/residue: 0.3975 time to fit residues: 166.5568 Evaluate side-chains 242 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 3.472 ------------------------------------------------------------------------------- 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 608 VAL Chi-restraints excluded: chain A residue 765 LEU 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 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 1292 TRP Chi-restraints excluded: chain D residue 1356 VAL 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 68 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 261 optimal weight: 30.0000 chunk 36 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D1656 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.086261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063532 restraints weight = 127083.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.065252 restraints weight = 74265.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.065595 restraints weight = 48682.804| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 30334 Z= 0.131 Angle : 0.555 7.976 41488 Z= 0.285 Chirality : 0.040 0.190 4733 Planarity : 0.004 0.045 4953 Dihedral : 14.149 160.799 5192 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 1.67 % Allowed : 10.98 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3370 helix: 0.97 (0.13), residues: 1616 sheet: -0.83 (0.25), residues: 372 loop : -0.42 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 814 HIS 0.005 0.001 HIS D1185 PHE 0.016 0.001 PHE D 370 TYR 0.022 0.001 TYR D1328 ARG 0.004 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 1454) hydrogen bonds : angle 4.59318 ( 4120) covalent geometry : bond 0.00296 (30334) covalent geometry : angle 0.55476 (41488) *********************** 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 283 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8121 (mmm) cc_final: 0.7580 (mmm) REVERT: A 362 PHE cc_start: 0.6449 (OUTLIER) cc_final: 0.6022 (m-10) REVERT: A 531 TYR cc_start: 0.8688 (t80) cc_final: 0.8461 (t80) REVERT: A 589 PHE cc_start: 0.7748 (t80) cc_final: 0.7473 (t80) REVERT: A 893 MET cc_start: 0.7950 (mpp) cc_final: 0.7624 (mpp) REVERT: A 907 TYR cc_start: 0.8086 (m-80) cc_final: 0.7767 (m-80) REVERT: A 922 MET cc_start: 0.8738 (mmm) cc_final: 0.8468 (mmm) REVERT: A 939 MET cc_start: 0.7576 (tpp) cc_final: 0.7356 (mmp) REVERT: A 1209 MET cc_start: 0.7781 (ptt) cc_final: 0.7392 (ptt) REVERT: B 352 LYS cc_start: 0.6652 (mmmt) cc_final: 0.6402 (mmmt) REVERT: C 266 LYS cc_start: 0.8586 (mppt) cc_final: 0.8302 (mppt) REVERT: D 208 MET cc_start: 0.7737 (mmm) cc_final: 0.7254 (mmp) REVERT: D 212 MET cc_start: 0.9063 (ppp) cc_final: 0.8835 (ppp) REVERT: D 344 MET cc_start: 0.7991 (ppp) cc_final: 0.7629 (ppp) REVERT: D 719 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8125 (mtm-85) REVERT: D 747 ASN cc_start: 0.8364 (t0) cc_final: 0.8054 (t0) REVERT: D 805 MET cc_start: 0.7627 (ppp) cc_final: 0.7034 (ppp) REVERT: D 992 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8114 (mm) REVERT: D 1207 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8024 (p90) REVERT: D 1328 TYR cc_start: 0.6175 (OUTLIER) cc_final: 0.5801 (t80) REVERT: D 1614 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8439 (t0) REVERT: D 1681 MET cc_start: 0.7884 (tmm) cc_final: 0.7521 (tmm) REVERT: D 1689 MET cc_start: 0.7365 (tmm) cc_final: 0.7025 (mmm) outliers start: 51 outliers final: 29 residues processed: 265 average time/residue: 0.3882 time to fit residues: 171.8907 Evaluate side-chains 249 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 3.326 ------------------------------------------------------------------------------- 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 386 ILE 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 1185 HIS Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain D residue 1207 PHE 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 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 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 116 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 230 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 288 optimal weight: 30.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 422 GLN A 884 GLN ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.085257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.062419 restraints weight = 126996.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064074 restraints weight = 75886.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.064584 restraints weight = 49074.107| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 30334 Z= 0.180 Angle : 0.596 13.426 41488 Z= 0.306 Chirality : 0.041 0.366 4733 Planarity : 0.004 0.045 4953 Dihedral : 14.170 160.864 5192 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 2.03 % Allowed : 12.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3370 helix: 0.88 (0.13), residues: 1618 sheet: -0.95 (0.25), residues: 380 loop : -0.46 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 97 HIS 0.011 0.001 HIS C 224 PHE 0.016 0.001 PHE D 370 TYR 0.047 0.002 TYR A 519 ARG 0.003 0.000 ARG D 496 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 1454) hydrogen bonds : angle 4.66939 ( 4120) covalent geometry : bond 0.00408 (30334) covalent geometry : angle 0.59558 (41488) *********************** 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 279 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8452 (tp) cc_final: 0.8075 (tt) REVERT: A 344 MET cc_start: 0.8080 (mmm) cc_final: 0.7582 (mmm) REVERT: A 362 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.6230 (m-10) REVERT: A 531 TYR cc_start: 0.8704 (t80) cc_final: 0.8484 (t80) REVERT: A 589 PHE cc_start: 0.7706 (t80) cc_final: 0.7437 (t80) REVERT: A 939 MET cc_start: 0.7650 (tpp) cc_final: 0.7406 (mmp) REVERT: A 1209 MET cc_start: 0.7916 (ptt) cc_final: 0.7552 (ptt) REVERT: A 1343 TYR cc_start: 0.7905 (m-10) cc_final: 0.7229 (m-10) REVERT: B 352 LYS cc_start: 0.6718 (mmmt) cc_final: 0.6504 (mmmt) REVERT: C 218 MET cc_start: 0.8541 (ppp) cc_final: 0.8282 (ppp) REVERT: C 223 ARG cc_start: 0.8080 (ptt-90) cc_final: 0.7657 (tmm-80) REVERT: C 266 LYS cc_start: 0.8541 (mppt) cc_final: 0.8298 (mppt) REVERT: D 208 MET cc_start: 0.7823 (mmm) cc_final: 0.7298 (mmp) REVERT: D 344 MET cc_start: 0.8062 (ppp) cc_final: 0.7662 (ppp) REVERT: D 719 ARG cc_start: 0.8614 (mtm-85) cc_final: 0.8157 (mtm-85) REVERT: D 747 ASN cc_start: 0.8338 (t0) cc_final: 0.8003 (t0) REVERT: D 794 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8235 (pp20) REVERT: D 805 MET cc_start: 0.7599 (ppp) cc_final: 0.7014 (ppp) REVERT: D 992 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8156 (mm) REVERT: D 1328 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5712 (t80) REVERT: D 1614 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8369 (t0) REVERT: D 1681 MET cc_start: 0.7896 (tmm) cc_final: 0.7553 (tmm) REVERT: D 1689 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6969 (mmm) outliers start: 62 outliers final: 43 residues processed: 255 average time/residue: 0.3709 time to fit residues: 159.3173 Evaluate side-chains 252 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 2.999 ------------------------------------------------------------------------------- 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 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 999 MET 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 176 ILE 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 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 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 162 optimal weight: 20.0000 chunk 203 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 330 optimal weight: 0.0010 chunk 317 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.085937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.062922 restraints weight = 127535.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.065193 restraints weight = 71622.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065501 restraints weight = 45148.465| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30334 Z= 0.137 Angle : 0.575 13.390 41488 Z= 0.292 Chirality : 0.040 0.210 4733 Planarity : 0.004 0.048 4953 Dihedral : 14.118 160.550 5192 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.87 % Allowed : 13.01 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3370 helix: 1.00 (0.13), residues: 1610 sheet: -0.94 (0.25), residues: 380 loop : -0.43 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1634 HIS 0.007 0.001 HIS D 934 PHE 0.021 0.001 PHE D 981 TYR 0.021 0.001 TYR D1328 ARG 0.003 0.000 ARG D 764 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 1454) hydrogen bonds : angle 4.56725 ( 4120) covalent geometry : bond 0.00312 (30334) covalent geometry : angle 0.57501 (41488) *********************** 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 280 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.8986 (ttp) cc_final: 0.8667 (ttp) REVERT: A 344 MET cc_start: 0.8088 (mmm) cc_final: 0.7588 (mmm) REVERT: A 362 PHE cc_start: 0.6518 (OUTLIER) cc_final: 0.6201 (m-10) REVERT: A 372 MET cc_start: 0.8031 (mpp) cc_final: 0.7614 (mpp) REVERT: A 589 PHE cc_start: 0.7690 (t80) cc_final: 0.7403 (t80) REVERT: A 849 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8045 (mtp) REVERT: A 908 MET cc_start: 0.5393 (mmt) cc_final: 0.5041 (mmt) REVERT: A 922 MET cc_start: 0.8459 (mmm) cc_final: 0.8154 (mmm) REVERT: A 1209 MET cc_start: 0.7889 (ptt) cc_final: 0.7490 (ptt) REVERT: A 1343 TYR cc_start: 0.7831 (m-10) cc_final: 0.7222 (m-10) REVERT: C 219 ARG cc_start: 0.8321 (tpt-90) cc_final: 0.7961 (tpp80) REVERT: C 223 ARG cc_start: 0.8005 (ptt-90) cc_final: 0.7586 (tmm-80) REVERT: C 266 LYS cc_start: 0.8552 (mppt) cc_final: 0.8322 (mppt) REVERT: D 75 MET cc_start: 0.8274 (ttp) cc_final: 0.7809 (tmm) REVERT: D 208 MET cc_start: 0.7835 (mmm) cc_final: 0.7302 (mmp) REVERT: D 344 MET cc_start: 0.7974 (ppp) cc_final: 0.7566 (ppp) REVERT: D 719 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8199 (mtm-85) REVERT: D 747 ASN cc_start: 0.8350 (t0) cc_final: 0.7993 (t0) REVERT: D 794 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8257 (pp20) REVERT: D 805 MET cc_start: 0.7596 (ppp) cc_final: 0.7026 (ppp) REVERT: D 939 MET cc_start: 0.4373 (ppp) cc_final: 0.1963 (mmt) REVERT: D 992 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7979 (mm) REVERT: D 1614 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8367 (t0) REVERT: D 1681 MET cc_start: 0.7941 (tmm) cc_final: 0.7618 (tmm) REVERT: D 1689 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6969 (mmm) outliers start: 57 outliers final: 43 residues processed: 264 average time/residue: 0.3763 time to fit residues: 167.6737 Evaluate side-chains 260 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 3.348 ------------------------------------------------------------------------------- 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 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 953 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1355 CYS Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain D residue 42 LEU 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 386 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 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 1356 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain D residue 1451 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 299 optimal weight: 10.0000 chunk 303 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.085474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.062402 restraints weight = 128173.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.064482 restraints weight = 74628.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.064810 restraints weight = 46494.426| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 30334 Z= 0.163 Angle : 0.597 17.777 41488 Z= 0.301 Chirality : 0.041 0.329 4733 Planarity : 0.004 0.046 4953 Dihedral : 14.081 160.471 5192 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 2.26 % Allowed : 13.27 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3370 helix: 0.96 (0.13), residues: 1611 sheet: -1.01 (0.24), residues: 383 loop : -0.47 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1634 HIS 0.008 0.001 HIS C 224 PHE 0.026 0.001 PHE D 981 TYR 0.024 0.001 TYR A 531 ARG 0.003 0.000 ARG D 496 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 1454) hydrogen bonds : angle 4.58753 ( 4120) covalent geometry : bond 0.00370 (30334) covalent geometry : angle 0.59749 (41488) *********************** 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 288 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 219 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8461 (tp) cc_final: 0.8062 (tt) REVERT: A 322 MET cc_start: 0.9041 (ttp) cc_final: 0.8610 (ttp) REVERT: A 344 MET cc_start: 0.8088 (mmm) cc_final: 0.7591 (mmm) REVERT: A 360 MET cc_start: 0.7827 (tpt) cc_final: 0.7091 (mtm) REVERT: A 362 PHE cc_start: 0.6568 (OUTLIER) cc_final: 0.6238 (m-10) REVERT: A 372 MET cc_start: 0.8115 (mpp) cc_final: 0.7628 (mpp) REVERT: A 849 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8133 (mtp) REVERT: A 908 MET cc_start: 0.5557 (mmt) cc_final: 0.5181 (mmt) REVERT: A 1209 MET cc_start: 0.7934 (ptt) cc_final: 0.7577 (ptt) REVERT: A 1371 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: B 352 LYS cc_start: 0.6944 (mmmt) cc_final: 0.6362 (mmmt) REVERT: C 218 MET cc_start: 0.8501 (ppp) cc_final: 0.8189 (ppp) REVERT: C 219 ARG cc_start: 0.8341 (tpt-90) cc_final: 0.7948 (tpp80) REVERT: C 222 ASP cc_start: 0.8788 (m-30) cc_final: 0.8480 (m-30) REVERT: C 223 ARG cc_start: 0.8030 (ptt-90) cc_final: 0.7649 (tmm-80) REVERT: C 266 LYS cc_start: 0.8535 (mppt) cc_final: 0.8309 (mppt) REVERT: D 75 MET cc_start: 0.8248 (ttp) cc_final: 0.7801 (tmm) REVERT: D 208 MET cc_start: 0.7915 (mmm) cc_final: 0.7381 (mmp) REVERT: D 344 MET cc_start: 0.8061 (ppp) cc_final: 0.7633 (ppp) REVERT: D 719 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8427 (mtm-85) REVERT: D 747 ASN cc_start: 0.8384 (t0) cc_final: 0.8038 (t0) REVERT: D 794 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8276 (pp20) REVERT: D 805 MET cc_start: 0.7592 (ppp) cc_final: 0.7020 (ppp) REVERT: D 939 MET cc_start: 0.4358 (ppp) cc_final: 0.2163 (mmm) REVERT: D 992 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7934 (mm) REVERT: D 1002 LEU cc_start: 0.8991 (tt) cc_final: 0.8718 (tp) REVERT: D 1003 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7546 (mm) REVERT: D 1328 TYR cc_start: 0.6349 (OUTLIER) cc_final: 0.5720 (t80) REVERT: D 1614 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8389 (t0) REVERT: D 1681 MET cc_start: 0.7954 (tmm) cc_final: 0.7613 (tmm) REVERT: D 1689 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6913 (mmm) outliers start: 69 outliers final: 53 residues processed: 265 average time/residue: 0.4557 time to fit residues: 206.2384 Evaluate side-chains 270 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 3.358 ------------------------------------------------------------------------------- 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 309 ILE 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 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 832 VAL Chi-restraints excluded: chain A residue 849 MET 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 1355 CYS Chi-restraints excluded: chain A residue 1371 GLU 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 247 TYR 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 176 ILE 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 506 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 895 VAL Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1003 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 1514 CYS 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 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 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 190 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 284 optimal weight: 0.2980 chunk 209 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 428 ASN ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** 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 = 0.3848 r_free = 0.3848 target = 0.085090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.061826 restraints weight = 128280.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.064332 restraints weight = 72957.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.064517 restraints weight = 44988.041| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30334 Z= 0.177 Angle : 0.609 12.614 41488 Z= 0.308 Chirality : 0.041 0.242 4733 Planarity : 0.004 0.049 4953 Dihedral : 14.060 160.234 5192 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 2.33 % Allowed : 13.93 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3370 helix: 0.88 (0.13), residues: 1626 sheet: -1.02 (0.24), residues: 383 loop : -0.55 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1634 HIS 0.009 0.001 HIS C 224 PHE 0.016 0.001 PHE D 370 TYR 0.024 0.002 TYR A 531 ARG 0.004 0.000 ARG D 496 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 1454) hydrogen bonds : angle 4.62300 ( 4120) covalent geometry : bond 0.00403 (30334) covalent geometry : angle 0.60939 (41488) *********************** 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 289 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 218 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.9049 (ttp) cc_final: 0.8648 (ttp) REVERT: A 344 MET cc_start: 0.8089 (mmm) cc_final: 0.7588 (mmm) REVERT: A 360 MET cc_start: 0.7682 (tpt) cc_final: 0.7089 (mtm) REVERT: A 362 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.6353 (m-10) REVERT: A 372 MET cc_start: 0.8028 (mpp) cc_final: 0.7562 (mpp) REVERT: A 849 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8141 (mtp) REVERT: A 893 MET cc_start: 0.8008 (mpp) cc_final: 0.7805 (mpp) REVERT: A 908 MET cc_start: 0.5559 (mmt) cc_final: 0.5142 (mmt) REVERT: A 1209 MET cc_start: 0.7987 (ptt) cc_final: 0.7655 (ptt) REVERT: A 1343 TYR cc_start: 0.8040 (m-10) cc_final: 0.7561 (m-10) REVERT: A 1371 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: B 352 LYS cc_start: 0.6973 (mmmt) cc_final: 0.6437 (mmmt) REVERT: C 200 LYS cc_start: 0.9280 (tppt) cc_final: 0.8946 (mttm) REVERT: C 218 MET cc_start: 0.8522 (ppp) cc_final: 0.8262 (ppp) REVERT: C 219 ARG cc_start: 0.8331 (tpt-90) cc_final: 0.7940 (tpp80) REVERT: C 223 ARG cc_start: 0.8054 (ptt-90) cc_final: 0.7639 (tmm-80) REVERT: C 266 LYS cc_start: 0.8580 (mppt) cc_final: 0.8351 (mppt) REVERT: D 75 MET cc_start: 0.8210 (ttp) cc_final: 0.7930 (ttp) REVERT: D 208 MET cc_start: 0.7911 (mmm) cc_final: 0.7368 (mmp) REVERT: D 344 MET cc_start: 0.8084 (ppp) cc_final: 0.7646 (ppp) REVERT: D 719 ARG cc_start: 0.8754 (mtm-85) cc_final: 0.8426 (mtm-85) REVERT: D 747 ASN cc_start: 0.8383 (t0) cc_final: 0.8038 (t0) REVERT: D 794 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8288 (pp20) REVERT: D 805 MET cc_start: 0.7602 (ppp) cc_final: 0.7035 (ppp) REVERT: D 852 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6904 (m-10) REVERT: D 992 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7911 (mm) REVERT: D 1003 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7567 (mm) REVERT: D 1259 ASP cc_start: 0.7949 (p0) cc_final: 0.7738 (m-30) REVERT: D 1328 TYR cc_start: 0.6290 (OUTLIER) cc_final: 0.5693 (t80) REVERT: D 1681 MET cc_start: 0.7969 (tmm) cc_final: 0.7618 (tmm) REVERT: D 1689 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6897 (mmm) REVERT: E 246 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7147 (pm20) REVERT: E 309 MET cc_start: 0.9148 (mmp) cc_final: 0.8919 (mmp) outliers start: 71 outliers final: 54 residues processed: 265 average time/residue: 0.4481 time to fit residues: 201.6386 Evaluate side-chains 274 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 211 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 221 VAL 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 404 LEU 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 849 MET 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 1355 CYS Chi-restraints excluded: chain A residue 1371 GLU 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 247 TYR 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 176 ILE 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 506 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 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 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 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 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 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 69 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 299 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 chunk 256 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 270 optimal weight: 10.0000 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.086011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.062874 restraints weight = 126639.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.065459 restraints weight = 71833.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.065564 restraints weight = 44592.964| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 30334 Z= 0.129 Angle : 0.588 13.072 41488 Z= 0.294 Chirality : 0.040 0.232 4733 Planarity : 0.004 0.049 4953 Dihedral : 13.972 159.970 5192 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 2.23 % Allowed : 14.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3370 helix: 0.91 (0.13), residues: 1635 sheet: -0.88 (0.25), residues: 375 loop : -0.49 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1634 HIS 0.007 0.001 HIS C 224 PHE 0.018 0.001 PHE D 981 TYR 0.023 0.001 TYR A 531 ARG 0.003 0.000 ARG D 496 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 1454) hydrogen bonds : angle 4.51888 ( 4120) covalent geometry : bond 0.00294 (30334) covalent geometry : angle 0.58815 (41488) *********************** 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 295 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 227 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.8157 (tt) cc_final: 0.7872 (tp) REVERT: A 322 MET cc_start: 0.9044 (ttp) cc_final: 0.8641 (ttp) REVERT: A 344 MET cc_start: 0.8056 (mmm) cc_final: 0.7558 (mmm) REVERT: A 360 MET cc_start: 0.7649 (tpt) cc_final: 0.7302 (mtm) REVERT: A 362 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.6369 (m-10) REVERT: A 849 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8056 (mtp) REVERT: A 893 MET cc_start: 0.7936 (mpp) cc_final: 0.7734 (mpp) REVERT: A 939 MET cc_start: 0.7439 (tpp) cc_final: 0.7112 (mmp) REVERT: A 1209 MET cc_start: 0.7923 (ptt) cc_final: 0.7564 (ptt) REVERT: A 1343 TYR cc_start: 0.7941 (m-10) cc_final: 0.7491 (m-10) REVERT: A 1371 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: A 1417 MET cc_start: 0.1379 (tpt) cc_final: 0.0861 (tpt) REVERT: C 200 LYS cc_start: 0.9272 (tppt) cc_final: 0.8896 (mttm) REVERT: C 218 MET cc_start: 0.8471 (ppp) cc_final: 0.8184 (ppp) REVERT: C 219 ARG cc_start: 0.8355 (tpt-90) cc_final: 0.7957 (tpp80) REVERT: C 222 ASP cc_start: 0.8771 (m-30) cc_final: 0.8481 (m-30) REVERT: C 223 ARG cc_start: 0.8011 (ptt-90) cc_final: 0.7625 (tmm-80) REVERT: D 75 MET cc_start: 0.8170 (ttp) cc_final: 0.7892 (ttp) REVERT: D 208 MET cc_start: 0.7850 (mmm) cc_final: 0.7316 (mmp) REVERT: D 344 MET cc_start: 0.7994 (ppp) cc_final: 0.7572 (ppp) REVERT: D 620 MET cc_start: 0.7638 (mmm) cc_final: 0.7389 (mmm) REVERT: D 719 ARG cc_start: 0.8842 (mtm-85) cc_final: 0.8624 (mtm-85) REVERT: D 747 ASN cc_start: 0.8313 (t0) cc_final: 0.7980 (t0) REVERT: D 794 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8300 (pp20) REVERT: D 805 MET cc_start: 0.7582 (ppp) cc_final: 0.7018 (ppp) REVERT: D 852 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: D 939 MET cc_start: 0.4552 (ppp) cc_final: 0.2435 (mmt) REVERT: D 986 TRP cc_start: 0.7591 (m-90) cc_final: 0.7282 (m-90) REVERT: D 992 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7889 (mm) REVERT: D 1003 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7565 (mm) REVERT: D 1328 TYR cc_start: 0.6262 (OUTLIER) cc_final: 0.5630 (t80) REVERT: D 1681 MET cc_start: 0.7912 (tmm) cc_final: 0.7567 (tmm) REVERT: D 1689 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6852 (mmm) REVERT: E 246 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7181 (pm20) REVERT: E 256 ASP cc_start: 0.7981 (t0) cc_final: 0.7744 (t0) outliers start: 68 outliers final: 55 residues processed: 273 average time/residue: 0.3829 time to fit residues: 176.7940 Evaluate side-chains 278 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 214 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 211 VAL 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 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 849 MET 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 1355 CYS Chi-restraints excluded: chain A residue 1371 GLU 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 247 TYR 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 219 THR Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 386 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 799 LEU Chi-restraints excluded: chain D residue 852 PHE Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 903 THR 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 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 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 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 7 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 214 optimal weight: 7.9990 chunk 234 optimal weight: 0.8980 chunk 318 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.086098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.063086 restraints weight = 125840.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.065326 restraints weight = 69454.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.065582 restraints weight = 45692.211| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30334 Z= 0.126 Angle : 0.599 14.521 41488 Z= 0.297 Chirality : 0.040 0.223 4733 Planarity : 0.004 0.051 4953 Dihedral : 13.923 160.361 5192 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 2.06 % Allowed : 14.65 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3370 helix: 0.97 (0.13), residues: 1636 sheet: -0.87 (0.25), residues: 376 loop : -0.47 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1634 HIS 0.007 0.001 HIS C 224 PHE 0.019 0.001 PHE D 981 TYR 0.023 0.001 TYR A 531 ARG 0.003 0.000 ARG A 998 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 1454) hydrogen bonds : angle 4.49650 ( 4120) covalent geometry : bond 0.00289 (30334) covalent geometry : angle 0.59862 (41488) ********************** 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: 63 poor density : 223 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.9003 (ttp) cc_final: 0.8593 (ttp) REVERT: A 344 MET cc_start: 0.8041 (mmm) cc_final: 0.7542 (mmm) REVERT: A 360 MET cc_start: 0.7664 (tpt) cc_final: 0.7318 (mtm) REVERT: A 362 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6357 (m-10) REVERT: A 849 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8064 (mtp) REVERT: A 893 MET cc_start: 0.7912 (mpp) cc_final: 0.7703 (mpp) REVERT: A 1209 MET cc_start: 0.7944 (ptt) cc_final: 0.7539 (ptt) REVERT: A 1343 TYR cc_start: 0.7865 (m-10) cc_final: 0.7325 (m-10) REVERT: A 1371 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: A 1417 MET cc_start: 0.1411 (tpt) cc_final: 0.0904 (tpt) REVERT: C 218 MET cc_start: 0.8419 (ppp) cc_final: 0.8088 (ppp) REVERT: C 219 ARG cc_start: 0.8317 (tpt-90) cc_final: 0.7946 (tpp80) REVERT: C 255 MET cc_start: 0.8861 (mpp) cc_final: 0.8643 (ppp) REVERT: D 75 MET cc_start: 0.8194 (ttp) cc_final: 0.7862 (tpp) REVERT: D 208 MET cc_start: 0.7853 (mmm) cc_final: 0.7315 (mmp) REVERT: D 344 MET cc_start: 0.8021 (ppp) cc_final: 0.7593 (ppp) REVERT: D 465 GLU cc_start: 0.6620 (pt0) cc_final: 0.6416 (pt0) REVERT: D 620 MET cc_start: 0.7703 (mmm) cc_final: 0.7354 (mmm) REVERT: D 719 ARG cc_start: 0.8841 (mtm-85) cc_final: 0.8623 (mtm-85) REVERT: D 747 ASN cc_start: 0.8307 (t0) cc_final: 0.7991 (t0) REVERT: D 794 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8328 (pp20) REVERT: D 805 MET cc_start: 0.7542 (ppp) cc_final: 0.6972 (ppp) REVERT: D 852 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.6718 (m-10) REVERT: D 939 MET cc_start: 0.4952 (ppp) cc_final: 0.2630 (mmt) REVERT: D 986 TRP cc_start: 0.7698 (OUTLIER) cc_final: 0.7491 (m-90) REVERT: D 992 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7886 (mm) REVERT: D 1003 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7546 (mm) REVERT: D 1328 TYR cc_start: 0.6244 (OUTLIER) cc_final: 0.5620 (t80) REVERT: D 1681 MET cc_start: 0.7935 (tmm) cc_final: 0.7590 (tmm) REVERT: D 1689 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6862 (mmm) REVERT: E 246 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7146 (pm20) REVERT: E 256 ASP cc_start: 0.7946 (t0) cc_final: 0.7711 (t0) outliers start: 63 outliers final: 50 residues processed: 264 average time/residue: 0.3603 time to fit residues: 161.8430 Evaluate side-chains 278 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 218 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 211 VAL 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 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 849 MET 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 1355 CYS Chi-restraints excluded: chain A residue 1371 GLU 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 247 TYR 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 219 THR Chi-restraints excluded: chain D residue 386 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 903 THR Chi-restraints excluded: chain D residue 934 HIS Chi-restraints excluded: chain D residue 986 TRP 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 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 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 303 ILE 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 235 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 237 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.086920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.063997 restraints weight = 125463.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.066245 restraints weight = 69306.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.066462 restraints weight = 47976.801| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 30334 Z= 0.108 Angle : 0.579 12.915 41488 Z= 0.287 Chirality : 0.040 0.210 4733 Planarity : 0.004 0.051 4953 Dihedral : 13.871 160.417 5192 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 2.00 % Allowed : 14.81 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3370 helix: 1.06 (0.13), residues: 1628 sheet: -0.75 (0.25), residues: 370 loop : -0.40 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1634 HIS 0.006 0.001 HIS D 934 PHE 0.023 0.001 PHE D 981 TYR 0.023 0.001 TYR A 531 ARG 0.003 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 1454) hydrogen bonds : angle 4.39565 ( 4120) covalent geometry : bond 0.00242 (30334) covalent geometry : angle 0.57913 (41488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9231.23 seconds wall clock time: 163 minutes 11.90 seconds (9791.90 seconds total)