Starting phenix.real_space_refine on Thu Mar 5 04:45:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpw_22425/03_2026/7jpw_22425.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpw_22425/03_2026/7jpw_22425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jpw_22425/03_2026/7jpw_22425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpw_22425/03_2026/7jpw_22425.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpw_22425/03_2026/7jpw_22425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpw_22425/03_2026/7jpw_22425.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 10 5.49 5 S 109 5.16 5 C 12126 2.51 5 N 2985 2.21 5 O 3349 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18583 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 9009 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 1078} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "A" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 444 Unusual residues: {' CA': 1, '3PE': 9, 'PC1': 1, 'VFY': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.19, per 1000 atoms: 0.28 Number of scatterers: 18583 At special positions: 0 Unit cell: (144.82, 137.022, 158.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 109 16.00 P 10 15.00 F 3 9.00 O 3349 8.00 N 2985 7.00 C 12126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.02 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.02 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.04 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 961.7 milliseconds 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 17 sheets defined 52.9% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 52 through 70 removed outlier: 3.962A pdb=" N ILE A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 4.261A pdb=" N ASP A 77 " --> pdb=" O MET A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.809A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 103 removed outlier: 3.617A pdb=" N VAL A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 140 removed outlier: 3.535A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.678A pdb=" N PHE A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 196 through 218 removed outlier: 3.769A pdb=" N PHE A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.718A pdb=" N VAL A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.550A pdb=" N PHE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 345 removed outlier: 3.879A pdb=" N LYS A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 450 removed outlier: 4.266A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 486 removed outlier: 4.057A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N MET A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.636A pdb=" N TYR A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 492 " --> pdb=" O ARG A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 492' Processing helix chain 'A' and resid 495 through 498 Processing helix chain 'A' and resid 499 through 512 removed outlier: 3.712A pdb=" N VAL A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 526 Processing helix chain 'A' and resid 526 through 541 removed outlier: 3.656A pdb=" N ILE A 530 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 4.495A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.611A pdb=" N LEU A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.685A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 636 removed outlier: 3.996A pdb=" N LEU A 636 " --> pdb=" O TYR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 647 removed outlier: 3.573A pdb=" N PHE A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 656 removed outlier: 3.691A pdb=" N ILE A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 653 " --> pdb=" O ASN A 649 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 672 Processing helix chain 'A' and resid 801 through 806 Processing helix chain 'A' and resid 808 through 818 removed outlier: 3.613A pdb=" N SER A 812 " --> pdb=" O PHE A 808 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 845 removed outlier: 4.036A pdb=" N TYR A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 835 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 893 through 899 removed outlier: 3.999A pdb=" N ARG A 897 " --> pdb=" O VAL A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 906 through 911 removed outlier: 3.644A pdb=" N ARG A 910 " --> pdb=" O ARG A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.523A pdb=" N CYS A 920 " --> pdb=" O HIS A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 951 removed outlier: 3.825A pdb=" N THR A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A 944 " --> pdb=" O PHE A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1015 through 1025 removed outlier: 3.554A pdb=" N LEU A1019 " --> pdb=" O GLY A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1040 No H-bonds generated for 'chain 'A' and resid 1038 through 1040' Processing helix chain 'A' and resid 1041 through 1052 removed outlier: 3.935A pdb=" N PHE A1045 " --> pdb=" O MET A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1069 removed outlier: 4.051A pdb=" N VAL A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1095 Processing helix chain 'A' and resid 1105 through 1116 removed outlier: 4.268A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1137 removed outlier: 4.283A pdb=" N ALA A1126 " --> pdb=" O TYR A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1173 removed outlier: 3.944A pdb=" N ALA A1171 " --> pdb=" O LEU A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1206 removed outlier: 3.635A pdb=" N ILE A1191 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A1192 " --> pdb=" O LEU A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1242 removed outlier: 3.985A pdb=" N VAL A1240 " --> pdb=" O ARG A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1249 removed outlier: 3.940A pdb=" N SER A1248 " --> pdb=" O LYS A1245 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A1249 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1265 removed outlier: 3.798A pdb=" N PHE A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1289 removed outlier: 4.212A pdb=" N ALA A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A1273 " --> pdb=" O TYR A1269 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1322 Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1356 through 1383 removed outlier: 3.607A pdb=" N ILE A1362 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1395 through 1410 removed outlier: 3.799A pdb=" N LEU A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1428 Processing helix chain 'E' and resid 6 through 26 removed outlier: 3.800A pdb=" N ARG E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 127 Processing helix chain 'E' and resid 136 through 164 removed outlier: 3.716A pdb=" N ALA E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 204 Processing helix chain 'F' and resid 29 through 53 Processing helix chain 'F' and resid 53 through 65 removed outlier: 4.058A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN F 65 " --> pdb=" O TYR F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 109 removed outlier: 3.734A pdb=" N ARG F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.545A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 Processing helix chain 'F' and resid 239 through 242 Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 283 removed outlier: 3.821A pdb=" N LYS F 272 " --> pdb=" O GLY F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 334 through 346 removed outlier: 3.576A pdb=" N GLY F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 removed outlier: 3.655A pdb=" N PHE F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 408 Processing helix chain 'F' and resid 420 through 426 removed outlier: 3.610A pdb=" N GLN F 426 " --> pdb=" O ARG F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 431 removed outlier: 3.549A pdb=" N ASP F 430 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 439 Processing helix chain 'F' and resid 481 through 484 removed outlier: 3.743A pdb=" N GLN F 484 " --> pdb=" O LEU F 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 481 through 484' Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 542 through 546 Processing helix chain 'F' and resid 571 through 582 removed outlier: 3.704A pdb=" N GLU F 575 " --> pdb=" O ASP F 571 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP F 582 " --> pdb=" O ASN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 650 removed outlier: 3.714A pdb=" N THR F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 654 removed outlier: 7.145A pdb=" N ASP F 654 " --> pdb=" O LEU F 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 651 through 654' Processing helix chain 'F' and resid 655 through 660 removed outlier: 3.673A pdb=" N SER F 659 " --> pdb=" O ASN F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 693 Processing helix chain 'F' and resid 701 through 722 Processing helix chain 'F' and resid 723 through 726 Processing helix chain 'F' and resid 748 through 754 removed outlier: 3.659A pdb=" N GLU F 753 " --> pdb=" O GLU F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 763 Processing helix chain 'F' and resid 764 through 773 removed outlier: 3.512A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 830 Processing helix chain 'F' and resid 877 through 881 Processing helix chain 'F' and resid 882 through 892 Processing helix chain 'F' and resid 1045 through 1050 removed outlier: 3.647A pdb=" N MET F1049 " --> pdb=" O ASP F1045 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 955 through 957 Processing sheet with id=AA3, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA4, first strand: chain 'E' and resid 34 through 35 removed outlier: 3.527A pdb=" N SER E 81 " --> pdb=" O ILE E 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=AA6, first strand: chain 'F' and resid 124 through 125 removed outlier: 6.287A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.914A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER F 495 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU F 460 " --> pdb=" O SER F 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.914A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER F 495 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU F 460 " --> pdb=" O SER F 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'F' and resid 300 through 302 removed outlier: 8.007A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE F 359 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS F 358 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N PHE F 387 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR F 364 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N TYR F 411 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N TYR F 413 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR F 388 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE F 415 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER F 390 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 523 through 525 removed outlier: 5.962A pdb=" N ALA F 516 " --> pdb=" O LEU F 524 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 540 through 541 Processing sheet with id=AB4, first strand: chain 'F' and resid 662 through 664 removed outlier: 4.089A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS F 818 " --> pdb=" O LYS F 733 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 662 through 664 removed outlier: 4.089A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 803 through 804 Processing sheet with id=AB7, first strand: chain 'F' and resid 862 through 864 removed outlier: 6.534A pdb=" N ILE F 855 " --> pdb=" O LEU F 863 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 895 through 907 removed outlier: 5.204A pdb=" N PHE F 897 " --> pdb=" O PHE F 985 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE F 985 " --> pdb=" O PHE F 897 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS F 899 " --> pdb=" O GLN F 983 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLN F 983 " --> pdb=" O LYS F 899 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR F 901 " --> pdb=" O GLN F 981 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN F 981 " --> pdb=" O TYR F 901 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR F 903 " --> pdb=" O THR F 979 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR F 979 " --> pdb=" O TYR F 903 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2981 1.31 - 1.45: 5361 1.45 - 1.58: 10467 1.58 - 1.72: 20 1.72 - 1.86: 168 Bond restraints: 18997 Sorted by residual: bond pdb=" C05 VFY A1912 " pdb=" C06 VFY A1912 " ideal model delta sigma weight residual 1.375 1.532 -0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C09 VFY A1912 " pdb=" C11 VFY A1912 " ideal model delta sigma weight residual 1.381 1.522 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C21 3PE A1904 " pdb=" O21 3PE A1904 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C21 3PE A1906 " pdb=" O21 3PE A1906 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C21 3PE A1907 " pdb=" O21 3PE A1907 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 18992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 24482 2.20 - 4.41: 1000 4.41 - 6.61: 141 6.61 - 8.81: 35 8.81 - 11.01: 21 Bond angle restraints: 25679 Sorted by residual: angle pdb=" C SER E 81 " pdb=" N TYR E 82 " pdb=" CA TYR E 82 " ideal model delta sigma weight residual 121.29 132.21 -10.92 1.74e+00 3.30e-01 3.94e+01 angle pdb=" N VAL A 661 " pdb=" CA VAL A 661 " pdb=" C VAL A 661 " ideal model delta sigma weight residual 113.71 107.85 5.86 9.50e-01 1.11e+00 3.80e+01 angle pdb=" C TYR A 541 " pdb=" N TRP A 542 " pdb=" CA TRP A 542 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" N LEU A 522 " pdb=" CA LEU A 522 " pdb=" C LEU A 522 " ideal model delta sigma weight residual 111.36 105.62 5.74 1.09e+00 8.42e-01 2.77e+01 angle pdb=" N PHE A 536 " pdb=" CA PHE A 536 " pdb=" C PHE A 536 " ideal model delta sigma weight residual 111.28 116.17 -4.89 1.09e+00 8.42e-01 2.01e+01 ... (remaining 25674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 9520 17.76 - 35.53: 1304 35.53 - 53.29: 473 53.29 - 71.06: 118 71.06 - 88.82: 29 Dihedral angle restraints: 11444 sinusoidal: 4828 harmonic: 6616 Sorted by residual: dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual -86.00 -146.18 60.18 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CA ASP F 227 " pdb=" C ASP F 227 " pdb=" N ASN F 228 " pdb=" CA ASN F 228 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASP F 518 " pdb=" C ASP F 518 " pdb=" N PRO F 519 " pdb=" CA PRO F 519 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 11441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1936 0.056 - 0.112: 765 0.112 - 0.168: 127 0.168 - 0.224: 18 0.224 - 0.281: 2 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA TRP A 542 " pdb=" N TRP A 542 " pdb=" C TRP A 542 " pdb=" CB TRP A 542 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA PRO A 268 " pdb=" N PRO A 268 " pdb=" C PRO A 268 " pdb=" CB PRO A 268 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASN F 379 " pdb=" N ASN F 379 " pdb=" C ASN F 379 " pdb=" CB ASN F 379 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2845 not shown) Planarity restraints: 3203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 81 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C SER E 81 " -0.051 2.00e-02 2.50e+03 pdb=" O SER E 81 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR E 82 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 74 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO A 75 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 51 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO A 52 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.034 5.00e-02 4.00e+02 ... (remaining 3200 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 363 2.63 - 3.20: 17206 3.20 - 3.77: 27347 3.77 - 4.33: 39651 4.33 - 4.90: 65719 Nonbonded interactions: 150286 Sorted by model distance: nonbonded pdb=" OD2 ASP F 711 " pdb=" OG1 THR F 739 " model vdw 2.068 3.040 nonbonded pdb=" N 3PE A1906 " pdb=" O11 3PE A1906 " model vdw 2.079 3.120 nonbonded pdb=" N 3PE A1911 " pdb=" O14 3PE A1911 " model vdw 2.079 3.120 nonbonded pdb=" O SER A1232 " pdb=" OG SER A1232 " model vdw 2.105 3.040 nonbonded pdb=" OH TYR F 452 " pdb=" OG1 THR F 463 " model vdw 2.121 3.040 ... (remaining 150281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.700 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.015 0.274 19011 Z= 0.676 Angle : 1.060 11.014 25705 Z= 0.555 Chirality : 0.058 0.281 2848 Planarity : 0.006 0.062 3203 Dihedral : 19.261 88.820 7133 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.64 % Favored : 90.27 % Rotamer: Outliers : 11.04 % Allowed : 20.28 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.14), residues: 2222 helix: -2.69 (0.12), residues: 1094 sheet: -2.28 (0.30), residues: 219 loop : -3.51 (0.16), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 505 TYR 0.023 0.003 TYR A1334 PHE 0.027 0.003 PHE F 157 TRP 0.024 0.003 TRP A1016 HIS 0.007 0.001 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.01489 (18997) covalent geometry : angle 1.05950 (25679) SS BOND : bond 0.00414 ( 13) SS BOND : angle 1.60441 ( 26) hydrogen bonds : bond 0.18801 ( 837) hydrogen bonds : angle 7.37635 ( 2441) Misc. bond : bond 0.27449 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 208 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.5991 (pt0) REVERT: A 100 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5909 (tp30) REVERT: A 447 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8111 (tp) REVERT: A 449 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8574 (mt) REVERT: A 510 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5313 (tm-30) REVERT: A 565 LEU cc_start: 0.9131 (tt) cc_final: 0.8913 (tp) REVERT: A 666 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.5297 (mp0) REVERT: A 936 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8423 (m) REVERT: A 984 GLU cc_start: 0.7498 (tt0) cc_final: 0.7223 (tt0) REVERT: A 1036 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8668 (m-40) REVERT: A 1096 ARG cc_start: 0.6380 (mtp180) cc_final: 0.6142 (mtt-85) REVERT: A 1383 ASN cc_start: 0.7939 (m110) cc_final: 0.7736 (m110) REVERT: A 1427 ARG cc_start: 0.4105 (OUTLIER) cc_final: 0.2343 (mpp80) REVERT: E 5 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7030 (tp30) REVERT: E 59 LYS cc_start: 0.2835 (OUTLIER) cc_final: 0.1760 (mtpt) REVERT: E 130 ARG cc_start: 0.6490 (ttp-110) cc_final: 0.5832 (mtm110) REVERT: E 133 ARG cc_start: 0.3090 (mmt180) cc_final: 0.2885 (mmt180) REVERT: E 164 ARG cc_start: 0.4629 (OUTLIER) cc_final: 0.3609 (ppt170) REVERT: F 88 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8840 (ttmm) REVERT: F 158 ARG cc_start: 0.8002 (mpp80) cc_final: 0.7546 (mtm-85) REVERT: F 256 MET cc_start: 0.9068 (ttm) cc_final: 0.8868 (ttm) REVERT: F 330 LYS cc_start: 0.8538 (tttm) cc_final: 0.8255 (ttmt) REVERT: F 442 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8736 (mtpp) REVERT: F 908 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6119 (mm-30) REVERT: F 1020 MET cc_start: 0.7930 (ttp) cc_final: 0.7680 (ttp) outliers start: 220 outliers final: 156 residues processed: 408 average time/residue: 0.1272 time to fit residues: 81.1847 Evaluate side-chains 358 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 187 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 505 CYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1036 ASN Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1100 CYS Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1124 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1342 SER Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1421 ASP Chi-restraints excluded: chain A residue 1423 VAL Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 442 LYS Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 596 SER Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 630 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 672 ASP Chi-restraints excluded: chain F residue 678 ASN Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 711 ASP Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 770 SER Chi-restraints excluded: chain F residue 775 ASN Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 881 ILE Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 908 GLU Chi-restraints excluded: chain F residue 976 SER Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 239 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 453 HIS A 803 ASN A 909 ASN A 958 ASN A 999 ASN A1087 GLN A1138 GLN A1154 ASN A1183 ASN A1383 ASN A1398 HIS E 209 GLN F 56 GLN F 164 GLN F 169 HIS F 470 ASN F 511 ASN F 551 GLN F 556 GLN F 655 ASN F 679 ASN F 685 ASN F 720 GLN F 888 HIS F 988 ASN F1039 GLN F1065 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104156 restraints weight = 44607.691| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.76 r_work: 0.2958 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19011 Z= 0.128 Angle : 0.593 7.564 25705 Z= 0.306 Chirality : 0.042 0.166 2848 Planarity : 0.005 0.060 3203 Dihedral : 15.101 83.879 3164 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.62 % Allowed : 22.54 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.16), residues: 2222 helix: -0.76 (0.15), residues: 1099 sheet: -1.81 (0.31), residues: 218 loop : -2.57 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 138 TYR 0.026 0.001 TYR F 629 PHE 0.016 0.001 PHE F 515 TRP 0.019 0.001 TRP F 187 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00265 (18997) covalent geometry : angle 0.59166 (25679) SS BOND : bond 0.00366 ( 13) SS BOND : angle 1.19204 ( 26) hydrogen bonds : bond 0.04051 ( 837) hydrogen bonds : angle 4.53474 ( 2441) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 237 time to evaluate : 0.758 Fit side-chains REVERT: A 49 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.5649 (mp0) REVERT: A 54 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5986 (pp20) REVERT: A 74 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8340 (mtm) REVERT: A 100 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6193 (tp30) REVERT: A 108 TYR cc_start: 0.7274 (m-80) cc_final: 0.6897 (m-80) REVERT: A 201 LEU cc_start: 0.9129 (tt) cc_final: 0.8860 (tp) REVERT: A 341 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7478 (ttp80) REVERT: A 479 MET cc_start: 0.4692 (ppp) cc_final: 0.4298 (ppp) REVERT: A 510 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.5618 (tm-30) REVERT: A 666 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5027 (mp0) REVERT: A 910 ARG cc_start: 0.7073 (mtm-85) cc_final: 0.6829 (mtm-85) REVERT: A 919 GLN cc_start: 0.4806 (OUTLIER) cc_final: 0.3915 (mm-40) REVERT: A 941 MET cc_start: 0.8819 (mtp) cc_final: 0.8610 (mtp) REVERT: A 958 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8419 (m110) REVERT: A 984 GLU cc_start: 0.8163 (tt0) cc_final: 0.7873 (tt0) REVERT: A 1096 ARG cc_start: 0.6533 (mtp180) cc_final: 0.6319 (mtt-85) REVERT: A 1165 MET cc_start: 0.8494 (tmm) cc_final: 0.8115 (tmm) REVERT: A 1186 ASP cc_start: 0.8379 (m-30) cc_final: 0.8154 (m-30) REVERT: A 1421 ASP cc_start: 0.2316 (OUTLIER) cc_final: 0.1480 (t70) REVERT: E 10 ARG cc_start: 0.6494 (mtm180) cc_final: 0.6154 (mmm160) REVERT: E 31 HIS cc_start: 0.6464 (OUTLIER) cc_final: 0.6091 (t-90) REVERT: E 130 ARG cc_start: 0.6719 (ttp-110) cc_final: 0.6497 (mtm110) REVERT: E 133 ARG cc_start: 0.3219 (mmt180) cc_final: 0.2986 (mmt180) REVERT: F 205 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8901 (tt) REVERT: F 230 ARG cc_start: 0.6038 (OUTLIER) cc_final: 0.5647 (tpt170) REVERT: F 248 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8487 (tm-30) REVERT: F 330 LYS cc_start: 0.9123 (tttm) cc_final: 0.8690 (ttmt) REVERT: F 711 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.8013 (t70) REVERT: F 817 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8683 (tt) REVERT: F 1020 MET cc_start: 0.8485 (ttp) cc_final: 0.8157 (ttp) REVERT: F 1032 ARG cc_start: 0.7141 (ptp90) cc_final: 0.6940 (ptt-90) outliers start: 112 outliers final: 60 residues processed: 332 average time/residue: 0.1302 time to fit residues: 66.5580 Evaluate side-chains 270 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 197 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain A residue 1421 ASP Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 596 SER Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 711 ASP Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 44 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A1058 ASN E 209 GLN F 165 HIS F 308 HIS F 644 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109809 restraints weight = 33721.505| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 4.01 r_work: 0.2845 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19011 Z= 0.200 Angle : 0.633 8.941 25705 Z= 0.322 Chirality : 0.044 0.195 2848 Planarity : 0.005 0.056 3203 Dihedral : 13.668 82.850 2961 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 5.12 % Allowed : 22.99 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.17), residues: 2222 helix: -0.37 (0.15), residues: 1132 sheet: -1.59 (0.32), residues: 223 loop : -2.37 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 528 TYR 0.019 0.001 TYR F 629 PHE 0.016 0.001 PHE F 157 TRP 0.015 0.001 TRP A1016 HIS 0.013 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00479 (18997) covalent geometry : angle 0.63134 (25679) SS BOND : bond 0.00302 ( 13) SS BOND : angle 1.61628 ( 26) hydrogen bonds : bond 0.04345 ( 837) hydrogen bonds : angle 4.39652 ( 2441) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 208 time to evaluate : 0.572 Fit side-chains REVERT: A 49 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.5762 (mp0) REVERT: A 53 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: A 54 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.5994 (pp20) REVERT: A 74 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.8783 (mtm) REVERT: A 100 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6265 (tp30) REVERT: A 113 HIS cc_start: 0.4448 (OUTLIER) cc_final: 0.3805 (p-80) REVERT: A 201 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8843 (tp) REVERT: A 479 MET cc_start: 0.4689 (ppp) cc_final: 0.4316 (ppp) REVERT: A 484 TYR cc_start: 0.5444 (OUTLIER) cc_final: 0.4235 (t80) REVERT: A 510 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5605 (tm-30) REVERT: A 666 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5095 (mp0) REVERT: A 910 ARG cc_start: 0.6981 (mtm-85) cc_final: 0.6622 (mtm-85) REVERT: A 919 GLN cc_start: 0.4634 (OUTLIER) cc_final: 0.3709 (mm-40) REVERT: A 941 MET cc_start: 0.8852 (mtp) cc_final: 0.8627 (mtp) REVERT: A 958 ASN cc_start: 0.8852 (m-40) cc_final: 0.8519 (m-40) REVERT: A 984 GLU cc_start: 0.8320 (tt0) cc_final: 0.7999 (tt0) REVERT: A 1063 PHE cc_start: 0.7690 (t80) cc_final: 0.7175 (t80) REVERT: A 1096 ARG cc_start: 0.6485 (mtp180) cc_final: 0.6268 (mtt-85) REVERT: A 1165 MET cc_start: 0.8442 (tmm) cc_final: 0.7986 (tmm) REVERT: A 1421 ASP cc_start: 0.2458 (OUTLIER) cc_final: 0.1690 (t70) REVERT: E 31 HIS cc_start: 0.6556 (OUTLIER) cc_final: 0.6129 (t-90) REVERT: E 207 MET cc_start: 0.7763 (mmm) cc_final: 0.7536 (mmt) REVERT: F 230 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5723 (tpt170) REVERT: F 330 LYS cc_start: 0.9100 (tttm) cc_final: 0.8615 (ttmt) REVERT: F 711 ASP cc_start: 0.8422 (t70) cc_final: 0.8172 (t70) REVERT: F 817 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8653 (tt) outliers start: 102 outliers final: 68 residues processed: 292 average time/residue: 0.1285 time to fit residues: 58.3301 Evaluate side-chains 276 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 194 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain A residue 1421 ASP Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 168 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN E 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102420 restraints weight = 50699.746| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.92 r_work: 0.2939 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19011 Z= 0.127 Angle : 0.561 7.816 25705 Z= 0.286 Chirality : 0.041 0.162 2848 Planarity : 0.004 0.056 3203 Dihedral : 12.737 84.753 2951 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.42 % Allowed : 23.54 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.17), residues: 2222 helix: 0.11 (0.16), residues: 1124 sheet: -1.37 (0.33), residues: 222 loop : -2.15 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 528 TYR 0.019 0.001 TYR F 629 PHE 0.019 0.001 PHE F 689 TRP 0.015 0.001 TRP F 187 HIS 0.010 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00296 (18997) covalent geometry : angle 0.56000 (25679) SS BOND : bond 0.00270 ( 13) SS BOND : angle 1.18287 ( 26) hydrogen bonds : bond 0.03546 ( 837) hydrogen bonds : angle 4.10412 ( 2441) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 215 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.5719 (mp0) REVERT: A 53 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6558 (m-80) REVERT: A 74 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8403 (mtm) REVERT: A 100 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6271 (tp30) REVERT: A 113 HIS cc_start: 0.4236 (OUTLIER) cc_final: 0.3528 (p-80) REVERT: A 140 GLU cc_start: 0.7886 (pt0) cc_final: 0.7457 (tm-30) REVERT: A 201 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8785 (tp) REVERT: A 484 TYR cc_start: 0.5422 (OUTLIER) cc_final: 0.4245 (t80) REVERT: A 510 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5689 (tm-30) REVERT: A 910 ARG cc_start: 0.7187 (mtm-85) cc_final: 0.6965 (mtm-85) REVERT: A 916 HIS cc_start: 0.4799 (t-90) cc_final: 0.2813 (p90) REVERT: A 919 GLN cc_start: 0.4493 (OUTLIER) cc_final: 0.3600 (mm-40) REVERT: A 984 GLU cc_start: 0.8219 (tt0) cc_final: 0.7891 (tt0) REVERT: A 1063 PHE cc_start: 0.7689 (t80) cc_final: 0.7337 (t80) REVERT: A 1121 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7004 (tm-30) REVERT: A 1165 MET cc_start: 0.8502 (tmm) cc_final: 0.8090 (tmm) REVERT: A 1239 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7106 (ptp-170) REVERT: A 1265 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: A 1412 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6387 (mm-30) REVERT: A 1421 ASP cc_start: 0.2354 (OUTLIER) cc_final: 0.1645 (t70) REVERT: E 191 LEU cc_start: 0.8672 (mt) cc_final: 0.8165 (tp) REVERT: E 207 MET cc_start: 0.7777 (mmm) cc_final: 0.7573 (mmt) REVERT: F 205 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8937 (tt) REVERT: F 330 LYS cc_start: 0.9044 (tttm) cc_final: 0.8614 (ttmt) REVERT: F 368 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: F 711 ASP cc_start: 0.8136 (t70) cc_final: 0.7902 (t70) outliers start: 88 outliers final: 51 residues processed: 288 average time/residue: 0.1232 time to fit residues: 55.7525 Evaluate side-chains 260 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 195 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1265 GLN Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain A residue 1421 ASP Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 161 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN E 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099969 restraints weight = 54695.463| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.03 r_work: 0.2893 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19011 Z= 0.181 Angle : 0.601 9.173 25705 Z= 0.305 Chirality : 0.043 0.159 2848 Planarity : 0.004 0.056 3203 Dihedral : 12.540 83.924 2932 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.92 % Allowed : 24.20 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 2222 helix: 0.26 (0.16), residues: 1106 sheet: -1.37 (0.32), residues: 229 loop : -2.05 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1249 TYR 0.015 0.001 TYR F 629 PHE 0.021 0.001 PHE E 182 TRP 0.014 0.001 TRP A1016 HIS 0.011 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00433 (18997) covalent geometry : angle 0.60010 (25679) SS BOND : bond 0.00249 ( 13) SS BOND : angle 1.28465 ( 26) hydrogen bonds : bond 0.03915 ( 837) hydrogen bonds : angle 4.13833 ( 2441) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 205 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.5740 (mp0) REVERT: A 53 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: A 62 PHE cc_start: 0.8517 (t80) cc_final: 0.8291 (t80) REVERT: A 74 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8748 (mtm) REVERT: A 100 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6233 (tp30) REVERT: A 140 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: A 201 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8747 (tp) REVERT: A 291 MET cc_start: 0.9084 (mtm) cc_final: 0.8858 (mtm) REVERT: A 484 TYR cc_start: 0.5418 (OUTLIER) cc_final: 0.4355 (t80) REVERT: A 510 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.5754 (tt0) REVERT: A 666 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5177 (mp0) REVERT: A 910 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6892 (mtm-85) REVERT: A 916 HIS cc_start: 0.4844 (t-90) cc_final: 0.2855 (p90) REVERT: A 919 GLN cc_start: 0.4655 (OUTLIER) cc_final: 0.3753 (mm-40) REVERT: A 984 GLU cc_start: 0.8286 (tt0) cc_final: 0.7975 (tt0) REVERT: A 1063 PHE cc_start: 0.7737 (t80) cc_final: 0.7329 (t80) REVERT: A 1121 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 1165 MET cc_start: 0.8510 (tmm) cc_final: 0.8054 (tmm) REVERT: A 1239 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7168 (ptp-170) REVERT: A 1265 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: A 1421 ASP cc_start: 0.2522 (OUTLIER) cc_final: 0.1870 (t70) REVERT: E 8 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6444 (ptpt) REVERT: E 207 MET cc_start: 0.7822 (mmm) cc_final: 0.7606 (mmt) REVERT: F 230 ARG cc_start: 0.6069 (OUTLIER) cc_final: 0.5575 (tpt170) REVERT: F 330 LYS cc_start: 0.9096 (tttm) cc_final: 0.8654 (ttmt) REVERT: F 638 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7612 (pt) REVERT: F 711 ASP cc_start: 0.8310 (t70) cc_final: 0.8101 (t70) REVERT: F 1020 MET cc_start: 0.8495 (ttp) cc_final: 0.8127 (ttp) outliers start: 98 outliers final: 65 residues processed: 284 average time/residue: 0.1215 time to fit residues: 54.0883 Evaluate side-chains 274 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 194 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1265 GLN Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain A residue 1421 ASP Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 638 ILE Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 95 optimal weight: 0.5980 chunk 199 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100604 restraints weight = 48749.654| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.82 r_work: 0.2902 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19011 Z= 0.161 Angle : 0.589 8.632 25705 Z= 0.299 Chirality : 0.042 0.165 2848 Planarity : 0.004 0.056 3203 Dihedral : 12.340 84.242 2930 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.87 % Allowed : 24.10 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.18), residues: 2222 helix: 0.37 (0.16), residues: 1110 sheet: -1.28 (0.32), residues: 228 loop : -2.03 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1249 TYR 0.013 0.001 TYR F 629 PHE 0.020 0.001 PHE F 689 TRP 0.013 0.001 TRP A1016 HIS 0.010 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00383 (18997) covalent geometry : angle 0.58797 (25679) SS BOND : bond 0.00250 ( 13) SS BOND : angle 1.19713 ( 26) hydrogen bonds : bond 0.03731 ( 837) hydrogen bonds : angle 4.08694 ( 2441) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 203 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.5670 (mp0) REVERT: A 51 LYS cc_start: 0.5295 (OUTLIER) cc_final: 0.5004 (ttpp) REVERT: A 53 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: A 62 PHE cc_start: 0.8459 (t80) cc_final: 0.8238 (t80) REVERT: A 74 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8948 (mtp) REVERT: A 100 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6188 (tp30) REVERT: A 140 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: A 201 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8812 (tp) REVERT: A 291 MET cc_start: 0.9098 (mtm) cc_final: 0.8844 (mtm) REVERT: A 484 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.4390 (t80) REVERT: A 510 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.5729 (tt0) REVERT: A 666 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5160 (mp0) REVERT: A 910 ARG cc_start: 0.7288 (mtm-85) cc_final: 0.6945 (mtm-85) REVERT: A 919 GLN cc_start: 0.4474 (OUTLIER) cc_final: 0.3607 (mm-40) REVERT: A 984 GLU cc_start: 0.8269 (tt0) cc_final: 0.7948 (tt0) REVERT: A 1063 PHE cc_start: 0.7679 (t80) cc_final: 0.7271 (t80) REVERT: A 1121 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6856 (tm-30) REVERT: A 1165 MET cc_start: 0.8495 (tmm) cc_final: 0.8024 (tmm) REVERT: A 1239 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7169 (ptp-170) REVERT: E 8 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6428 (ptpt) REVERT: E 207 MET cc_start: 0.7839 (mmm) cc_final: 0.7636 (mmt) REVERT: F 230 ARG cc_start: 0.5991 (OUTLIER) cc_final: 0.5509 (tpt170) REVERT: F 330 LYS cc_start: 0.9050 (tttm) cc_final: 0.8580 (ttmt) REVERT: F 638 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7593 (pt) REVERT: F 711 ASP cc_start: 0.8301 (t70) cc_final: 0.8038 (t70) REVERT: F 1002 CYS cc_start: 0.5578 (OUTLIER) cc_final: 0.4380 (p) REVERT: F 1020 MET cc_start: 0.8547 (ttp) cc_final: 0.8190 (ttp) outliers start: 97 outliers final: 62 residues processed: 285 average time/residue: 0.1218 time to fit residues: 54.6237 Evaluate side-chains 275 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 198 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 638 ILE Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 0.0270 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN E 209 GLN F 484 GLN F 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.150786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103278 restraints weight = 50839.906| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.90 r_work: 0.2953 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19011 Z= 0.113 Angle : 0.550 13.572 25705 Z= 0.277 Chirality : 0.041 0.165 2848 Planarity : 0.004 0.055 3203 Dihedral : 11.674 88.674 2924 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.02 % Allowed : 24.70 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.18), residues: 2222 helix: 0.69 (0.16), residues: 1103 sheet: -1.19 (0.32), residues: 234 loop : -1.88 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 528 TYR 0.012 0.001 TYR F 629 PHE 0.023 0.001 PHE F 689 TRP 0.015 0.001 TRP F 187 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00261 (18997) covalent geometry : angle 0.54955 (25679) SS BOND : bond 0.00242 ( 13) SS BOND : angle 1.00790 ( 26) hydrogen bonds : bond 0.03218 ( 837) hydrogen bonds : angle 3.92620 ( 2441) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 207 time to evaluate : 0.804 Fit side-chains REVERT: A 49 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.5565 (mp0) REVERT: A 51 LYS cc_start: 0.5460 (OUTLIER) cc_final: 0.5245 (ttpp) REVERT: A 53 PHE cc_start: 0.6756 (OUTLIER) cc_final: 0.6496 (m-80) REVERT: A 62 PHE cc_start: 0.8472 (t80) cc_final: 0.8263 (t80) REVERT: A 74 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8352 (mtm) REVERT: A 100 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6251 (tp30) REVERT: A 140 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: A 201 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8718 (tp) REVERT: A 291 MET cc_start: 0.9088 (mtm) cc_final: 0.8882 (mtm) REVERT: A 484 TYR cc_start: 0.5391 (OUTLIER) cc_final: 0.4304 (t80) REVERT: A 510 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5600 (tt0) REVERT: A 666 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5079 (mp0) REVERT: A 910 ARG cc_start: 0.7324 (mtm-85) cc_final: 0.6968 (mtm-85) REVERT: A 919 GLN cc_start: 0.4525 (OUTLIER) cc_final: 0.3672 (mm-40) REVERT: A 984 GLU cc_start: 0.8221 (tt0) cc_final: 0.7918 (tt0) REVERT: A 1063 PHE cc_start: 0.7563 (t80) cc_final: 0.7263 (t80) REVERT: A 1121 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6997 (tm-30) REVERT: A 1165 MET cc_start: 0.8515 (tmm) cc_final: 0.8065 (tmm) REVERT: A 1170 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 1265 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: E 8 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6373 (ptpt) REVERT: E 10 ARG cc_start: 0.6638 (mtp180) cc_final: 0.6143 (mmm160) REVERT: E 151 LEU cc_start: 0.8608 (mt) cc_final: 0.8299 (mm) REVERT: E 159 ARG cc_start: 0.6885 (ttt180) cc_final: 0.6572 (mtm180) REVERT: E 191 LEU cc_start: 0.8694 (mt) cc_final: 0.8012 (tp) REVERT: F 59 ASP cc_start: 0.8197 (t0) cc_final: 0.7734 (t0) REVERT: F 230 ARG cc_start: 0.5928 (OUTLIER) cc_final: 0.5509 (tpt170) REVERT: F 248 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8590 (tm-30) REVERT: F 330 LYS cc_start: 0.9035 (tttm) cc_final: 0.8605 (ttmt) REVERT: F 638 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7658 (pt) REVERT: F 711 ASP cc_start: 0.8166 (t70) cc_final: 0.7918 (t70) REVERT: F 997 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8558 (tp) REVERT: F 1002 CYS cc_start: 0.5678 (OUTLIER) cc_final: 0.4350 (p) REVERT: F 1020 MET cc_start: 0.8502 (ttp) cc_final: 0.8170 (ttp) outliers start: 80 outliers final: 53 residues processed: 275 average time/residue: 0.1334 time to fit residues: 57.8965 Evaluate side-chains 270 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 200 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1265 GLN Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 638 ILE Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 4 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 39 optimal weight: 0.0010 chunk 85 optimal weight: 9.9990 chunk 139 optimal weight: 0.0570 chunk 146 optimal weight: 0.5980 chunk 162 optimal weight: 0.4980 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN E 209 GLN F 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110314 restraints weight = 49296.965| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.74 r_work: 0.3064 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19011 Z= 0.094 Angle : 0.533 15.668 25705 Z= 0.266 Chirality : 0.040 0.161 2848 Planarity : 0.004 0.054 3203 Dihedral : 10.808 84.759 2911 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.16 % Allowed : 25.60 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.18), residues: 2222 helix: 0.92 (0.16), residues: 1110 sheet: -1.02 (0.33), residues: 228 loop : -1.65 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.010 0.001 TYR A1091 PHE 0.026 0.001 PHE F 689 TRP 0.015 0.001 TRP F 187 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00209 (18997) covalent geometry : angle 0.53259 (25679) SS BOND : bond 0.00207 ( 13) SS BOND : angle 0.90468 ( 26) hydrogen bonds : bond 0.02831 ( 837) hydrogen bonds : angle 3.79718 ( 2441) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.5823 (mp0) REVERT: A 51 LYS cc_start: 0.5626 (OUTLIER) cc_final: 0.5400 (ttpp) REVERT: A 53 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.6635 (m-80) REVERT: A 62 PHE cc_start: 0.8463 (t80) cc_final: 0.8241 (t80) REVERT: A 100 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6324 (tp30) REVERT: A 135 PHE cc_start: 0.7384 (t80) cc_final: 0.7114 (t80) REVERT: A 484 TYR cc_start: 0.5270 (OUTLIER) cc_final: 0.3974 (t80) REVERT: A 510 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.5551 (tt0) REVERT: A 614 GLU cc_start: 0.8336 (tp30) cc_final: 0.7632 (tp30) REVERT: A 910 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.6796 (mtm-85) REVERT: A 919 GLN cc_start: 0.4647 (OUTLIER) cc_final: 0.3785 (mm-40) REVERT: A 984 GLU cc_start: 0.8273 (tt0) cc_final: 0.7932 (tt0) REVERT: A 1063 PHE cc_start: 0.7484 (t80) cc_final: 0.7145 (t80) REVERT: A 1121 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7100 (tm-30) REVERT: A 1165 MET cc_start: 0.8502 (tmm) cc_final: 0.8118 (tmm) REVERT: A 1170 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7547 (mp) REVERT: E 10 ARG cc_start: 0.6641 (mtp180) cc_final: 0.6164 (mmm160) REVERT: E 151 LEU cc_start: 0.8604 (mt) cc_final: 0.8335 (mm) REVERT: E 159 ARG cc_start: 0.6938 (ttt180) cc_final: 0.6680 (mtm180) REVERT: E 191 LEU cc_start: 0.8634 (mt) cc_final: 0.8023 (tp) REVERT: F 59 ASP cc_start: 0.8182 (t0) cc_final: 0.7732 (t0) REVERT: F 330 LYS cc_start: 0.9005 (tttm) cc_final: 0.8683 (ttmt) REVERT: F 368 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: F 711 ASP cc_start: 0.8060 (t70) cc_final: 0.7828 (t70) REVERT: F 1002 CYS cc_start: 0.5648 (OUTLIER) cc_final: 0.4383 (p) REVERT: F 1020 MET cc_start: 0.8447 (ttp) cc_final: 0.8156 (ttp) REVERT: F 1071 TYR cc_start: 0.8200 (p90) cc_final: 0.7962 (p90) outliers start: 63 outliers final: 40 residues processed: 278 average time/residue: 0.1280 time to fit residues: 55.8792 Evaluate side-chains 262 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 177 optimal weight: 0.0170 chunk 83 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN F 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115339 restraints weight = 32855.172| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.58 r_work: 0.2931 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19011 Z= 0.109 Angle : 0.554 13.048 25705 Z= 0.275 Chirality : 0.041 0.168 2848 Planarity : 0.004 0.054 3203 Dihedral : 10.550 89.801 2891 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.91 % Allowed : 26.05 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.18), residues: 2222 helix: 0.99 (0.16), residues: 1116 sheet: -1.01 (0.32), residues: 232 loop : -1.61 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F1032 TYR 0.012 0.001 TYR A 108 PHE 0.024 0.001 PHE F 689 TRP 0.013 0.001 TRP F 187 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00254 (18997) covalent geometry : angle 0.55376 (25679) SS BOND : bond 0.00217 ( 13) SS BOND : angle 0.94391 ( 26) hydrogen bonds : bond 0.03036 ( 837) hydrogen bonds : angle 3.78489 ( 2441) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.5718 (mp0) REVERT: A 51 LYS cc_start: 0.5548 (OUTLIER) cc_final: 0.5280 (ttpp) REVERT: A 53 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6592 (m-80) REVERT: A 54 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6173 (pp20) REVERT: A 62 PHE cc_start: 0.8413 (t80) cc_final: 0.8170 (t80) REVERT: A 100 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6102 (tp30) REVERT: A 135 PHE cc_start: 0.7417 (t80) cc_final: 0.7133 (t80) REVERT: A 193 MET cc_start: 0.8250 (ptt) cc_final: 0.7886 (ptt) REVERT: A 201 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8650 (tp) REVERT: A 484 TYR cc_start: 0.5260 (OUTLIER) cc_final: 0.3987 (t80) REVERT: A 510 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5563 (tt0) REVERT: A 614 GLU cc_start: 0.8355 (tp30) cc_final: 0.7564 (tp30) REVERT: A 919 GLN cc_start: 0.4360 (OUTLIER) cc_final: 0.3611 (mm-40) REVERT: A 984 GLU cc_start: 0.8305 (tt0) cc_final: 0.7996 (tt0) REVERT: A 1063 PHE cc_start: 0.7503 (t80) cc_final: 0.7135 (t80) REVERT: A 1121 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 1165 MET cc_start: 0.8408 (tmm) cc_final: 0.8006 (tmm) REVERT: A 1170 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7473 (mp) REVERT: E 10 ARG cc_start: 0.6633 (mtp180) cc_final: 0.6107 (mmm160) REVERT: E 151 LEU cc_start: 0.8588 (mt) cc_final: 0.8320 (mm) REVERT: E 159 ARG cc_start: 0.6829 (ttt180) cc_final: 0.6592 (mtm180) REVERT: E 191 LEU cc_start: 0.8701 (mt) cc_final: 0.8071 (tp) REVERT: E 207 MET cc_start: 0.7885 (mmt) cc_final: 0.7669 (mmt) REVERT: E 216 MET cc_start: 0.6271 (tmm) cc_final: 0.5984 (tmm) REVERT: F 59 ASP cc_start: 0.8261 (t0) cc_final: 0.7781 (t0) REVERT: F 330 LYS cc_start: 0.9111 (tttm) cc_final: 0.8672 (ttmt) REVERT: F 368 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: F 711 ASP cc_start: 0.8234 (t70) cc_final: 0.7995 (t70) REVERT: F 1002 CYS cc_start: 0.5601 (OUTLIER) cc_final: 0.4183 (p) REVERT: F 1020 MET cc_start: 0.8568 (ttp) cc_final: 0.8290 (ttp) outliers start: 58 outliers final: 41 residues processed: 260 average time/residue: 0.1234 time to fit residues: 50.9927 Evaluate side-chains 262 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 190 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 218 optimal weight: 0.4980 chunk 65 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN F 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.105726 restraints weight = 45676.337| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.75 r_work: 0.2980 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19011 Z= 0.105 Angle : 0.556 14.862 25705 Z= 0.275 Chirality : 0.041 0.171 2848 Planarity : 0.004 0.053 3203 Dihedral : 10.396 85.382 2890 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.91 % Allowed : 25.90 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 2222 helix: 1.10 (0.16), residues: 1115 sheet: -0.98 (0.32), residues: 232 loop : -1.51 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F1032 TYR 0.012 0.001 TYR A1091 PHE 0.027 0.001 PHE A1205 TRP 0.014 0.001 TRP F 187 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00243 (18997) covalent geometry : angle 0.55510 (25679) SS BOND : bond 0.00210 ( 13) SS BOND : angle 0.93913 ( 26) hydrogen bonds : bond 0.02968 ( 837) hydrogen bonds : angle 3.74880 ( 2441) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.5781 (mp0) REVERT: A 51 LYS cc_start: 0.5521 (OUTLIER) cc_final: 0.5254 (ttpp) REVERT: A 53 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6586 (m-80) REVERT: A 54 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.6154 (pp20) REVERT: A 62 PHE cc_start: 0.8358 (t80) cc_final: 0.8102 (t80) REVERT: A 74 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8343 (mtm) REVERT: A 100 GLU cc_start: 0.6570 (mm-30) cc_final: 0.5929 (tp30) REVERT: A 135 PHE cc_start: 0.7409 (t80) cc_final: 0.7197 (t80) REVERT: A 193 MET cc_start: 0.8173 (ptt) cc_final: 0.7783 (ptt) REVERT: A 201 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8614 (tp) REVERT: A 484 TYR cc_start: 0.5223 (OUTLIER) cc_final: 0.4011 (t80) REVERT: A 510 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5529 (tt0) REVERT: A 614 GLU cc_start: 0.8289 (tp30) cc_final: 0.7479 (tp30) REVERT: A 666 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.4809 (mp0) REVERT: A 910 ARG cc_start: 0.7233 (mtm-85) cc_final: 0.7022 (mtm-85) REVERT: A 919 GLN cc_start: 0.4401 (OUTLIER) cc_final: 0.3654 (mm-40) REVERT: A 984 GLU cc_start: 0.8198 (tt0) cc_final: 0.7865 (tt0) REVERT: A 1031 MET cc_start: 0.9276 (mtp) cc_final: 0.8853 (mtp) REVERT: A 1063 PHE cc_start: 0.7431 (t80) cc_final: 0.7070 (t80) REVERT: A 1121 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 1165 MET cc_start: 0.8393 (tmm) cc_final: 0.7989 (tmm) REVERT: E 10 ARG cc_start: 0.6670 (mtp180) cc_final: 0.6108 (mmm160) REVERT: E 151 LEU cc_start: 0.8622 (mt) cc_final: 0.8356 (mm) REVERT: E 191 LEU cc_start: 0.8683 (mt) cc_final: 0.8065 (tp) REVERT: E 207 MET cc_start: 0.7829 (mmt) cc_final: 0.7619 (mmt) REVERT: E 216 MET cc_start: 0.6336 (tmm) cc_final: 0.6018 (tmm) REVERT: F 59 ASP cc_start: 0.8225 (t0) cc_final: 0.7738 (t0) REVERT: F 330 LYS cc_start: 0.9056 (tttm) cc_final: 0.8603 (ttmt) REVERT: F 368 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: F 711 ASP cc_start: 0.8165 (t70) cc_final: 0.7921 (t70) REVERT: F 1002 CYS cc_start: 0.5568 (OUTLIER) cc_final: 0.4249 (p) REVERT: F 1020 MET cc_start: 0.8489 (ttp) cc_final: 0.8203 (ttp) outliers start: 58 outliers final: 41 residues processed: 262 average time/residue: 0.1227 time to fit residues: 51.1878 Evaluate side-chains 265 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 212 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 169 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 168 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.102581 restraints weight = 52456.516| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.89 r_work: 0.2934 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19011 Z= 0.142 Angle : 0.583 13.494 25705 Z= 0.290 Chirality : 0.042 0.175 2848 Planarity : 0.004 0.053 3203 Dihedral : 10.517 85.338 2890 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.21 % Allowed : 25.70 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 2222 helix: 0.99 (0.16), residues: 1123 sheet: -0.97 (0.33), residues: 232 loop : -1.52 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F1032 TYR 0.010 0.001 TYR A1021 PHE 0.028 0.001 PHE A1205 TRP 0.012 0.001 TRP A1016 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00340 (18997) covalent geometry : angle 0.58232 (25679) SS BOND : bond 0.00238 ( 13) SS BOND : angle 1.05153 ( 26) hydrogen bonds : bond 0.03372 ( 837) hydrogen bonds : angle 3.84486 ( 2441) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4760.13 seconds wall clock time: 82 minutes 59.55 seconds (4979.55 seconds total)