Starting phenix.real_space_refine on Thu Mar 5 05:36:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpx_22426/03_2026/7jpx_22426_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpx_22426/03_2026/7jpx_22426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jpx_22426/03_2026/7jpx_22426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpx_22426/03_2026/7jpx_22426.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpx_22426/03_2026/7jpx_22426_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpx_22426/03_2026/7jpx_22426_neut.cif" } resolution = 2.9 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 11 5.49 5 S 110 5.16 5 Cl 1 4.86 5 C 12168 2.51 5 N 2984 2.21 5 O 3365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.01s 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: 18640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 9016 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 35, 'TRANS': 1080} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen planarities: 1 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: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 494 Unusual residues: {' CA': 1, '3PE': 9, '6UB': 1, 'PC1': 1, 'POV': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.60, per 1000 atoms: 0.30 Number of scatterers: 18640 At special positions: 0 Unit cell: (142.592, 138.136, 155.96, 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 Cl 1 17.00 S 110 16.00 P 11 15.00 O 3365 8.00 N 2984 7.00 C 12168 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=2.02 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=2.04 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=2.03 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=2.03 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: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4274 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 14 sheets defined 52.7% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.591A pdb=" N GLU A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.719A pdb=" N LEU A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 97 removed outlier: 3.866A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 143 removed outlier: 3.585A pdb=" N PHE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.617A pdb=" N PHE A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 4.102A pdb=" N VAL A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 removed outlier: 3.752A pdb=" N GLN A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 196 through 218 removed outlier: 3.698A 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: 3.611A pdb=" N VAL A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.567A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 345 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.815A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 457 through 485 removed outlier: 3.521A pdb=" N THR A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.511A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 removed outlier: 3.870A pdb=" N ASN A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 514 removed outlier: 3.764A pdb=" N ILE A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 4.047A pdb=" N VAL A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 535 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.665A pdb=" N LYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 581 removed outlier: 3.712A pdb=" N VAL A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.601A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 636 removed outlier: 3.613A pdb=" N LEU A 636 " --> pdb=" O PRO A 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 633 through 636' Processing helix chain 'A' and resid 637 through 656 removed outlier: 4.086A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 removed outlier: 3.853A pdb=" N SER A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 818 removed outlier: 3.585A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 846 removed outlier: 3.749A pdb=" N TYR A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 835 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.858A pdb=" N ASP A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 903 through 907 Processing helix chain 'A' and resid 911 through 922 Processing helix chain 'A' and resid 929 through 951 removed outlier: 3.694A pdb=" N VAL A 934 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 942 " --> pdb=" O LEU A 938 " (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: 3.562A pdb=" N LEU A1019 " --> pdb=" O GLY A1015 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A1025 " --> pdb=" O TYR A1021 " (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: 4.104A pdb=" N PHE A1045 " --> pdb=" O MET A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1061 Processing helix chain 'A' and resid 1061 through 1066 Processing helix chain 'A' and resid 1083 through 1095 removed outlier: 3.663A pdb=" N GLN A1087 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A1091 " --> pdb=" O GLN A1087 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A1092 " --> pdb=" O CYS A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1116 removed outlier: 3.531A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1137 removed outlier: 3.755A pdb=" N PHE A1125 " --> pdb=" O GLU A1121 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE A1128 " --> pdb=" O MET A1124 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A1133 " --> pdb=" O MET A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1173 removed outlier: 3.746A pdb=" N ILE A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A1152 " --> pdb=" O HIS A1148 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1202 removed outlier: 3.590A pdb=" N VAL A1197 " --> pdb=" O SER A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 3.512A pdb=" N LEU A1237 " --> pdb=" O PHE A1234 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A1239 " --> pdb=" O ARG A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1249 removed outlier: 3.725A pdb=" N LYS A1245 " --> pdb=" O ARG A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1266 removed outlier: 3.902A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1289 removed outlier: 3.964A pdb=" N ALA A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A1287 " --> pdb=" O VAL A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1322 Processing helix chain 'A' and resid 1324 through 1330 Processing helix chain 'A' and resid 1356 through 1382 removed outlier: 3.540A pdb=" N ILE A1372 " --> pdb=" O CYS A1368 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A1373 " --> pdb=" O ALA A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1395 through 1410 removed outlier: 3.700A pdb=" N LEU A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1426 removed outlier: 3.508A pdb=" N LEU A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 removed outlier: 3.668A pdb=" N ARG E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY E 19 " --> pdb=" O CYS E 15 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 28 " --> pdb=" O MET E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 removed outlier: 3.822A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 163 removed outlier: 3.661A pdb=" N ALA E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 204 removed outlier: 4.145A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 53 removed outlier: 3.513A pdb=" N GLY F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 74 through 110 removed outlier: 3.616A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.789A 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 251 removed outlier: 3.817A pdb=" N ALA F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 283 removed outlier: 3.626A 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 Processing helix chain 'F' and resid 371 through 379 Processing helix chain 'F' and resid 398 through 408 Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'F' and resid 420 through 425 Processing helix chain 'F' and resid 433 through 438 Processing helix chain 'F' and resid 439 through 444 removed outlier: 3.801A pdb=" N LYS F 442 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 444 " --> pdb=" O ASP F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 542 through 546 removed outlier: 4.222A pdb=" N ARG F 546 " --> pdb=" O LEU F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 566 Processing helix chain 'F' and resid 571 through 582 removed outlier: 3.647A pdb=" N GLU F 575 " --> pdb=" O ASP F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 651 removed outlier: 3.517A pdb=" N GLN F 644 " --> pdb=" O GLU F 640 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU F 651 " --> pdb=" O TYR F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 654 No H-bonds generated for 'chain 'F' and resid 652 through 654' Processing helix chain 'F' and resid 655 through 660 Processing helix chain 'F' and resid 678 through 693 Processing helix chain 'F' and resid 701 through 722 Processing helix chain 'F' and resid 764 through 773 Processing helix chain 'F' and resid 820 through 829 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 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 79 through 81 removed outlier: 4.278A pdb=" N ASN E 79 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR E 58 " --> pdb=" O ASN E 79 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 49 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR E 177 " --> pdb=" O VAL E 34 " (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 144 through 146 removed outlier: 6.146A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N VAL F 168 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 144 through 146 removed outlier: 6.146A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N VAL F 168 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'F' and resid 300 through 302 removed outlier: 6.791A pdb=" N MET F 256 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP F 255 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET F 361 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU F 257 " --> pdb=" O MET F 361 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N PHE F 363 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU F 259 " --> pdb=" O PHE F 363 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 523 through 525 removed outlier: 3.963A pdb=" N LEU F 525 " --> pdb=" O ALA F 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 540 through 541 removed outlier: 3.930A pdb=" N ILE F 541 " --> pdb=" O GLY F 910 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 661 through 664 removed outlier: 3.924A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS F 818 " --> pdb=" O LYS F 733 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ARG F 735 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY F 816 " --> pdb=" O ARG F 735 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL F 737 " --> pdb=" O VAL F 814 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL F 814 " --> pdb=" O VAL F 737 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR F 739 " --> pdb=" O PRO F 812 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LYS F 811 " --> pdb=" O ILE F 803 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE F 803 " --> pdb=" O LYS F 811 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA F 813 " --> pdb=" O VAL F 801 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 862 through 864 removed outlier: 6.482A pdb=" N ILE F 855 " --> pdb=" O LEU F 863 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 896 through 907 removed outlier: 4.372A pdb=" N GLN F 904 " --> pdb=" O CYS F 977 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS F 977 " --> pdb=" O GLN F 904 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL F 906 " --> pdb=" O GLN F 975 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN F 975 " --> pdb=" O VAL F 906 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) 883 hydrogen bonds defined for protein. 2510 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: 3.62 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2986 1.31 - 1.44: 5189 1.44 - 1.57: 10684 1.57 - 1.70: 23 1.70 - 1.83: 171 Bond restraints: 19053 Sorted by residual: bond pdb=" CAW 6UB A1913 " pdb=" CAY 6UB A1913 " ideal model delta sigma weight residual 1.357 1.526 -0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" CAT 6UB A1913 " pdb=" CAX 6UB A1913 " ideal model delta sigma weight residual 1.357 1.525 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C21 3PE A1902 " pdb=" O21 3PE A1902 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C21 3PE A1904 " pdb=" O21 3PE A1904 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C21 3PE A1903 " pdb=" O21 3PE A1903 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.70e+01 ... (remaining 19048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 25189 3.11 - 6.23: 473 6.23 - 9.34: 63 9.34 - 12.46: 18 12.46 - 15.57: 1 Bond angle restraints: 25744 Sorted by residual: angle pdb=" C THR A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.84 129.92 -10.08 1.25e+00 6.40e-01 6.51e+01 angle pdb=" N THR A 520 " pdb=" CA THR A 520 " pdb=" C THR A 520 " ideal model delta sigma weight residual 109.81 125.38 -15.57 2.21e+00 2.05e-01 4.97e+01 angle pdb=" N GLY F 177 " pdb=" CA GLY F 177 " pdb=" C GLY F 177 " ideal model delta sigma weight residual 114.48 107.34 7.14 1.19e+00 7.06e-01 3.60e+01 angle pdb=" N VAL F 894 " pdb=" CA VAL F 894 " pdb=" C VAL F 894 " ideal model delta sigma weight residual 113.39 105.55 7.84 1.47e+00 4.63e-01 2.85e+01 angle pdb=" N THR E 58 " pdb=" CA THR E 58 " pdb=" C THR E 58 " ideal model delta sigma weight residual 110.17 118.20 -8.03 1.51e+00 4.39e-01 2.83e+01 ... (remaining 25739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.84: 10495 29.84 - 59.68: 924 59.68 - 89.52: 71 89.52 - 119.36: 4 119.36 - 149.20: 1 Dihedral angle restraints: 11495 sinusoidal: 4874 harmonic: 6621 Sorted by residual: dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 80 " pdb=" CB CYS E 80 " ideal model delta sinusoidal sigma weight residual 93.00 13.67 79.33 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS F 999 " pdb=" SG CYS F 999 " pdb=" SG CYS F1029 " pdb=" CB CYS F1029 " ideal model delta sinusoidal sigma weight residual 93.00 39.88 53.12 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CA SER E 214 " pdb=" C SER E 214 " pdb=" N CYS E 215 " pdb=" CA CYS E 215 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 11492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2463 0.084 - 0.168: 362 0.168 - 0.252: 23 0.252 - 0.336: 1 0.336 - 0.420: 1 Chirality restraints: 2850 Sorted by residual: chirality pdb=" CA THR A 520 " pdb=" N THR A 520 " pdb=" C THR A 520 " pdb=" CB THR A 520 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CG LEU F 257 " pdb=" CB LEU F 257 " pdb=" CD1 LEU F 257 " pdb=" CD2 LEU F 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+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 2.47 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 2847 not shown) Planarity restraints: 3210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 530 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO F 531 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO F 531 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 531 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 267 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO A 268 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 155 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C LEU E 155 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU E 155 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU E 156 " -0.014 2.00e-02 2.50e+03 ... (remaining 3207 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 382 2.64 - 3.21: 16869 3.21 - 3.77: 27969 3.77 - 4.34: 40418 4.34 - 4.90: 66208 Nonbonded interactions: 151846 Sorted by model distance: nonbonded pdb=" N 3PE A1906 " pdb=" O11 3PE A1906 " model vdw 2.078 3.120 nonbonded pdb=" O ASN F 233 " pdb=" ND2 ASN F 233 " model vdw 2.078 3.120 nonbonded pdb=" N 3PE A1908 " pdb=" O14 3PE A1908 " model vdw 2.078 3.120 nonbonded pdb=" CG ARG E 55 " pdb=" O SER E 81 " model vdw 2.086 3.440 nonbonded pdb=" OH TYR F 452 " pdb=" OG1 THR F 463 " model vdw 2.096 3.040 ... (remaining 151841 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: 1.640 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.090 Process input model: 19.530 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.014 0.733 19067 Z= 0.786 Angle : 1.106 15.574 25770 Z= 0.579 Chirality : 0.059 0.420 2850 Planarity : 0.006 0.075 3210 Dihedral : 20.318 149.203 7182 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.22 % Favored : 91.51 % Rotamer: Outliers : 11.89 % Allowed : 22.52 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -4.18 (0.14), residues: 2227 helix: -2.70 (0.12), residues: 1120 sheet: -1.51 (0.32), residues: 208 loop : -3.03 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 735 TYR 0.029 0.003 TYR A1334 PHE 0.035 0.003 PHE F 157 TRP 0.020 0.003 TRP F 245 HIS 0.007 0.002 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.01333 (19053) covalent geometry : angle 1.10426 (25744) SS BOND : bond 0.00643 ( 13) SS BOND : angle 1.99895 ( 26) hydrogen bonds : bond 0.18889 ( 864) hydrogen bonds : angle 7.13957 ( 2510) Misc. bond : bond 0.73323 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 266 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.4759 (OUTLIER) cc_final: 0.4493 (pt) REVERT: A 62 PHE cc_start: 0.8472 (t80) cc_final: 0.8244 (t80) REVERT: A 80 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8681 (p0) REVERT: A 114 GLN cc_start: 0.5789 (tt0) cc_final: 0.5018 (tm-30) REVERT: A 190 PHE cc_start: 0.7311 (t80) cc_final: 0.6569 (m-80) REVERT: A 247 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6916 (ptp-170) REVERT: A 452 GLU cc_start: 0.7833 (tt0) cc_final: 0.7607 (tt0) REVERT: A 494 SER cc_start: 0.1341 (OUTLIER) cc_final: 0.1011 (m) REVERT: A 519 MET cc_start: 0.4256 (ttp) cc_final: 0.3980 (ttp) REVERT: A 540 LYS cc_start: 0.3659 (OUTLIER) cc_final: 0.2105 (ttpp) REVERT: A 554 ASN cc_start: 0.6322 (OUTLIER) cc_final: 0.6053 (m-40) REVERT: A 871 LEU cc_start: 0.4977 (OUTLIER) cc_final: 0.4609 (tp) REVERT: A 933 LEU cc_start: 0.7909 (mt) cc_final: 0.7697 (mm) REVERT: A 1041 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8727 (tpp) REVERT: A 1105 ASN cc_start: 0.5037 (t160) cc_final: 0.4450 (t0) REVERT: A 1147 ASN cc_start: 0.5119 (OUTLIER) cc_final: 0.4680 (m110) REVERT: A 1151 ASP cc_start: 0.8065 (t0) cc_final: 0.7607 (p0) REVERT: A 1196 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7357 (t0) REVERT: A 1272 LEU cc_start: 0.8608 (tp) cc_final: 0.8263 (mm) REVERT: A 1286 MET cc_start: 0.8883 (mtp) cc_final: 0.8671 (mtm) REVERT: A 1337 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8828 (tt) REVERT: A 1339 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.8008 (p0) REVERT: A 1384 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.5970 (t80) REVERT: E 79 ASN cc_start: 0.4992 (OUTLIER) cc_final: 0.4700 (p0) REVERT: E 81 SER cc_start: 0.4180 (OUTLIER) cc_final: 0.3929 (p) REVERT: E 127 MET cc_start: 0.7649 (ttp) cc_final: 0.6766 (tmt) REVERT: E 158 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6235 (mtm) REVERT: F 234 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6714 (mttt) REVERT: F 307 GLN cc_start: 0.8136 (mt0) cc_final: 0.7784 (mm110) REVERT: F 326 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8310 (m-40) REVERT: F 430 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7941 (m-30) REVERT: F 545 LYS cc_start: 0.8312 (mttm) cc_final: 0.8082 (mmtt) REVERT: F 674 LYS cc_start: 0.8107 (ptpp) cc_final: 0.7804 (ttmm) REVERT: F 804 TYR cc_start: 0.8263 (m-80) cc_final: 0.7848 (m-80) outliers start: 237 outliers final: 135 residues processed: 467 average time/residue: 0.4586 time to fit residues: 248.9639 Evaluate side-chains 387 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 233 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1147 ASN Chi-restraints excluded: chain A residue 1148 HIS Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 178 TYR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 655 ASN Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 881 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 994 SER Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1050 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 239 ASN A 277 ASN A 307 ASN A 455 ASN A 599 ASN A 869 ASN A 939 GLN A1037 ASN A1105 ASN A1138 GLN A1383 ASN A1419 HIS F 56 GLN F 165 HIS F 169 HIS F 233 ASN F 394 HIS F 450 ASN F 470 ASN F 483 ASN F 511 ASN F 551 GLN F 644 GLN F 655 ASN F 679 ASN F 685 ASN F 696 ASN F 806 GLN F 847 ASN F 866 ASN F1039 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115945 restraints weight = 37340.155| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.66 r_work: 0.3097 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19067 Z= 0.138 Angle : 0.652 11.890 25770 Z= 0.340 Chirality : 0.043 0.196 2850 Planarity : 0.005 0.067 3210 Dihedral : 16.049 123.817 3160 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 7.02 % Allowed : 26.58 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -2.16 (0.16), residues: 2227 helix: -0.81 (0.15), residues: 1120 sheet: -0.97 (0.33), residues: 207 loop : -2.28 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.024 0.001 TYR F 629 PHE 0.018 0.001 PHE F 993 TRP 0.016 0.001 TRP F 113 HIS 0.003 0.001 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.00303 (19053) covalent geometry : angle 0.64795 (25744) SS BOND : bond 0.00509 ( 13) SS BOND : angle 2.31700 ( 26) hydrogen bonds : bond 0.04480 ( 864) hydrogen bonds : angle 4.55310 ( 2510) Misc. bond : bond 0.00292 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 255 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7528 (tt0) REVERT: A 114 GLN cc_start: 0.5839 (tt0) cc_final: 0.4985 (tm-30) REVERT: A 190 PHE cc_start: 0.7160 (t80) cc_final: 0.6249 (m-10) REVERT: A 494 SER cc_start: 0.1469 (OUTLIER) cc_final: 0.1099 (m) REVERT: A 548 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6382 (tt) REVERT: A 670 LEU cc_start: 0.3989 (OUTLIER) cc_final: 0.3712 (tt) REVERT: A 983 MET cc_start: 0.8956 (ptm) cc_final: 0.8650 (ptp) REVERT: A 1028 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7772 (mm-30) REVERT: A 1051 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8477 (tp) REVERT: A 1105 ASN cc_start: 0.4774 (t0) cc_final: 0.4155 (t0) REVERT: A 1125 PHE cc_start: 0.6824 (m-10) cc_final: 0.6621 (m-10) REVERT: A 1145 GLU cc_start: 0.1566 (OUTLIER) cc_final: 0.0813 (mm-30) REVERT: A 1151 ASP cc_start: 0.8259 (t0) cc_final: 0.7510 (p0) REVERT: A 1196 ASP cc_start: 0.7789 (t70) cc_final: 0.7393 (t0) REVERT: A 1267 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7420 (mt) REVERT: A 1272 LEU cc_start: 0.8409 (tp) cc_final: 0.8098 (mm) REVERT: A 1276 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8586 (ttm) REVERT: A 1286 MET cc_start: 0.9176 (mtp) cc_final: 0.8886 (mtm) REVERT: A 1384 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.5989 (t80) REVERT: A 1388 THR cc_start: 0.8741 (m) cc_final: 0.8400 (p) REVERT: E 113 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7073 (m-80) REVERT: E 127 MET cc_start: 0.7790 (ttp) cc_final: 0.6680 (tmt) REVERT: E 158 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6453 (mmm) REVERT: E 191 LEU cc_start: 0.6613 (tp) cc_final: 0.6397 (tm) REVERT: F 205 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8408 (tt) REVERT: F 233 ASN cc_start: 0.4149 (OUTLIER) cc_final: 0.3274 (p0) REVERT: F 234 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6699 (mmtt) REVERT: F 307 GLN cc_start: 0.8400 (mt0) cc_final: 0.7890 (mm110) REVERT: F 442 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8819 (mtpt) REVERT: F 490 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8441 (mpt) REVERT: F 505 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7918 (ppt-90) REVERT: F 545 LYS cc_start: 0.8272 (mttm) cc_final: 0.7915 (mmtt) REVERT: F 674 LYS cc_start: 0.8111 (ptpp) cc_final: 0.7736 (ttmm) REVERT: F 711 ASP cc_start: 0.7599 (m-30) cc_final: 0.7375 (m-30) REVERT: F 792 GLU cc_start: 0.7989 (mp0) cc_final: 0.7749 (mt-10) REVERT: F 804 TYR cc_start: 0.8359 (m-80) cc_final: 0.8008 (m-80) REVERT: F 851 MET cc_start: 0.7041 (ptp) cc_final: 0.6566 (ptm) REVERT: F 1040 THR cc_start: 0.9065 (t) cc_final: 0.8655 (m) outliers start: 140 outliers final: 56 residues processed: 366 average time/residue: 0.4754 time to fit residues: 201.4628 Evaluate side-chains 310 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 239 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1276 MET Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 233 ASN Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 112 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 159 optimal weight: 0.0370 chunk 49 optimal weight: 0.1980 chunk 86 optimal weight: 5.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 143 ASN A 599 ASN ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN A1131 ASN A1265 GLN F 233 ASN F 483 ASN F 644 GLN F 806 GLN F 888 HIS F 975 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116531 restraints weight = 53047.686| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.96 r_work: 0.3076 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19067 Z= 0.154 Angle : 0.626 11.799 25770 Z= 0.326 Chirality : 0.043 0.242 2850 Planarity : 0.005 0.061 3210 Dihedral : 14.376 117.886 3002 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 7.07 % Allowed : 25.88 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.45 (0.17), residues: 2227 helix: -0.13 (0.15), residues: 1136 sheet: -0.79 (0.32), residues: 221 loop : -2.07 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F1032 TYR 0.020 0.001 TYR F 629 PHE 0.020 0.001 PHE F 157 TRP 0.014 0.001 TRP F 245 HIS 0.003 0.001 HIS F 888 Details of bonding type rmsd covalent geometry : bond 0.00363 (19053) covalent geometry : angle 0.62360 (25744) SS BOND : bond 0.00473 ( 13) SS BOND : angle 1.79088 ( 26) hydrogen bonds : bond 0.04230 ( 864) hydrogen bonds : angle 4.30835 ( 2510) Misc. bond : bond 0.00142 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 250 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7549 (tt0) REVERT: A 114 GLN cc_start: 0.5827 (tt0) cc_final: 0.4982 (tm-30) REVERT: A 190 PHE cc_start: 0.7166 (t80) cc_final: 0.6302 (m-10) REVERT: A 553 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6770 (mp) REVERT: A 869 ASN cc_start: 0.3879 (OUTLIER) cc_final: 0.3614 (m110) REVERT: A 983 MET cc_start: 0.8963 (ptm) cc_final: 0.8610 (ptp) REVERT: A 1028 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7988 (mm-30) REVERT: A 1051 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 1105 ASN cc_start: 0.4766 (t0) cc_final: 0.4263 (t0) REVERT: A 1151 ASP cc_start: 0.8110 (t0) cc_final: 0.7470 (p0) REVERT: A 1267 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7331 (mt) REVERT: A 1272 LEU cc_start: 0.8407 (tp) cc_final: 0.8097 (mm) REVERT: A 1286 MET cc_start: 0.9188 (mtp) cc_final: 0.8866 (mtm) REVERT: A 1287 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.8032 (mm-40) REVERT: A 1384 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.5775 (t80) REVERT: A 1388 THR cc_start: 0.8686 (m) cc_final: 0.8332 (p) REVERT: E 127 MET cc_start: 0.7760 (ttp) cc_final: 0.6645 (tmt) REVERT: E 158 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6535 (mmm) REVERT: E 219 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.6018 (pp20) REVERT: F 205 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8461 (tt) REVERT: F 234 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6582 (mttt) REVERT: F 307 GLN cc_start: 0.8445 (mt0) cc_final: 0.7933 (mm110) REVERT: F 381 ASP cc_start: 0.8596 (p0) cc_final: 0.8076 (p0) REVERT: F 505 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8003 (ppt-90) REVERT: F 545 LYS cc_start: 0.8211 (mttm) cc_final: 0.7845 (mmtt) REVERT: F 674 LYS cc_start: 0.8047 (ptpp) cc_final: 0.7556 (ttmm) REVERT: F 792 GLU cc_start: 0.7959 (mp0) cc_final: 0.7662 (mt-10) REVERT: F 804 TYR cc_start: 0.8426 (m-80) cc_final: 0.8135 (m-80) REVERT: F 1020 MET cc_start: 0.8308 (ttm) cc_final: 0.8105 (ttp) outliers start: 141 outliers final: 72 residues processed: 353 average time/residue: 0.4564 time to fit residues: 186.4128 Evaluate side-chains 316 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 233 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS 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 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 143 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 143 ASN ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN F 308 HIS F 483 ASN F 484 GLN F 644 GLN F 806 GLN F 975 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.168466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115975 restraints weight = 43751.231| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.76 r_work: 0.3100 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19067 Z= 0.142 Angle : 0.602 11.138 25770 Z= 0.311 Chirality : 0.043 0.259 2850 Planarity : 0.005 0.062 3210 Dihedral : 13.457 112.898 2981 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 7.97 % Allowed : 25.43 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.95 (0.17), residues: 2227 helix: 0.31 (0.15), residues: 1142 sheet: -0.58 (0.32), residues: 219 loop : -1.91 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F1032 TYR 0.019 0.001 TYR F 629 PHE 0.025 0.001 PHE A1364 TRP 0.013 0.001 TRP F 245 HIS 0.006 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00332 (19053) covalent geometry : angle 0.60081 (25744) SS BOND : bond 0.00346 ( 13) SS BOND : angle 1.46794 ( 26) hydrogen bonds : bond 0.03878 ( 864) hydrogen bonds : angle 4.13776 ( 2510) Misc. bond : bond 0.00099 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 247 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7593 (tt0) REVERT: A 114 GLN cc_start: 0.6139 (tt0) cc_final: 0.5312 (tm-30) REVERT: A 190 PHE cc_start: 0.6802 (t80) cc_final: 0.6248 (m-10) REVERT: A 241 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8668 (ptpt) REVERT: A 308 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: A 548 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6198 (tt) REVERT: A 553 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6644 (pp) REVERT: A 869 ASN cc_start: 0.3866 (OUTLIER) cc_final: 0.3627 (m110) REVERT: A 948 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: A 976 LYS cc_start: 0.8802 (mmpt) cc_final: 0.8185 (mtmt) REVERT: A 983 MET cc_start: 0.8933 (ptm) cc_final: 0.8707 (ptp) REVERT: A 1028 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7929 (mm-30) REVERT: A 1041 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.9008 (tpp) REVERT: A 1051 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8517 (tp) REVERT: A 1063 PHE cc_start: 0.7943 (m-80) cc_final: 0.7224 (t80) REVERT: A 1105 ASN cc_start: 0.4846 (t0) cc_final: 0.4357 (t0) REVERT: A 1151 ASP cc_start: 0.7996 (t0) cc_final: 0.7406 (p0) REVERT: A 1286 MET cc_start: 0.9150 (mtp) cc_final: 0.8864 (mtm) REVERT: A 1371 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.7967 (mp) REVERT: A 1384 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.6082 (t80) REVERT: E 58 THR cc_start: -0.0208 (OUTLIER) cc_final: -0.0426 (t) REVERT: E 113 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.6802 (m-80) REVERT: E 118 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6917 (tm) REVERT: E 127 MET cc_start: 0.7727 (ttp) cc_final: 0.6641 (tmt) REVERT: E 158 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6911 (mmm) REVERT: E 216 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5359 (tpt) REVERT: F 205 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8465 (tt) REVERT: F 234 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6461 (mmtt) REVERT: F 307 GLN cc_start: 0.8379 (mt0) cc_final: 0.7885 (mm110) REVERT: F 381 ASP cc_start: 0.8599 (p0) cc_final: 0.8130 (p0) REVERT: F 545 LYS cc_start: 0.8231 (mttm) cc_final: 0.7906 (mmtt) REVERT: F 674 LYS cc_start: 0.8042 (ptpp) cc_final: 0.7581 (ptmt) REVERT: F 793 SER cc_start: 0.8325 (m) cc_final: 0.8067 (t) REVERT: F 804 TYR cc_start: 0.8371 (m-80) cc_final: 0.8028 (m-80) outliers start: 159 outliers final: 80 residues processed: 362 average time/residue: 0.4852 time to fit residues: 202.4671 Evaluate side-chains 332 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 235 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 235 ILE 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 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 116 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 78 optimal weight: 0.0070 chunk 5 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN F 483 ASN F 644 GLN F 975 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.168983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118453 restraints weight = 48161.944| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.76 r_work: 0.3093 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19067 Z= 0.131 Angle : 0.584 9.642 25770 Z= 0.301 Chirality : 0.042 0.279 2850 Planarity : 0.004 0.059 3210 Dihedral : 12.859 108.824 2971 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 7.57 % Allowed : 25.98 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.65 (0.18), residues: 2227 helix: 0.60 (0.16), residues: 1144 sheet: -0.57 (0.33), residues: 225 loop : -1.81 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 341 TYR 0.018 0.001 TYR F 629 PHE 0.017 0.001 PHE F 157 TRP 0.013 0.001 TRP F 245 HIS 0.004 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00307 (19053) covalent geometry : angle 0.58334 (25744) SS BOND : bond 0.00438 ( 13) SS BOND : angle 1.11191 ( 26) hydrogen bonds : bond 0.03679 ( 864) hydrogen bonds : angle 4.03532 ( 2510) Misc. bond : bond 0.00094 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 245 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7421 (tt0) REVERT: A 114 GLN cc_start: 0.6037 (tt0) cc_final: 0.5290 (tm-30) REVERT: A 190 PHE cc_start: 0.6754 (t80) cc_final: 0.6376 (m-10) REVERT: A 308 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: A 483 MET cc_start: 0.2906 (OUTLIER) cc_final: 0.2691 (pp-130) REVERT: A 548 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6150 (tt) REVERT: A 553 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6672 (pp) REVERT: A 869 ASN cc_start: 0.3942 (OUTLIER) cc_final: 0.3726 (m110) REVERT: A 906 ARG cc_start: 0.4222 (OUTLIER) cc_final: 0.3530 (mtt180) REVERT: A 938 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8942 (mt) REVERT: A 948 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: A 976 LYS cc_start: 0.8825 (mmpt) cc_final: 0.8202 (mtmt) REVERT: A 983 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8621 (ptp) REVERT: A 1028 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7986 (mm-30) REVERT: A 1051 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 1096 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6426 (ttm-80) REVERT: A 1105 ASN cc_start: 0.4872 (t0) cc_final: 0.4385 (t0) REVERT: A 1151 ASP cc_start: 0.7998 (t0) cc_final: 0.7462 (p0) REVERT: A 1286 MET cc_start: 0.9127 (mtp) cc_final: 0.8874 (mtm) REVERT: A 1371 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 1384 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.6345 (t80) REVERT: E 113 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.6781 (m-80) REVERT: E 127 MET cc_start: 0.7746 (ttp) cc_final: 0.6648 (tmt) REVERT: E 142 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6895 (ptp) REVERT: E 216 MET cc_start: 0.5844 (OUTLIER) cc_final: 0.5297 (tpt) REVERT: E 219 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.5344 (pp20) REVERT: F 205 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8478 (tt) REVERT: F 234 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6412 (mttt) REVERT: F 286 SER cc_start: 0.8691 (p) cc_final: 0.8478 (t) REVERT: F 307 GLN cc_start: 0.8376 (mt0) cc_final: 0.7846 (mm110) REVERT: F 381 ASP cc_start: 0.8544 (p0) cc_final: 0.8127 (p0) REVERT: F 508 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8623 (mt) REVERT: F 545 LYS cc_start: 0.8267 (mttm) cc_final: 0.7912 (mmtt) REVERT: F 674 LYS cc_start: 0.8047 (ptpp) cc_final: 0.7586 (ptmt) REVERT: F 804 TYR cc_start: 0.8295 (m-80) cc_final: 0.7885 (m-80) REVERT: F 845 LYS cc_start: 0.6355 (mmtt) cc_final: 0.6130 (mmpt) REVERT: F 1024 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7767 (ttmt) outliers start: 151 outliers final: 71 residues processed: 351 average time/residue: 0.4436 time to fit residues: 180.7568 Evaluate side-chains 326 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 235 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1096 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 235 ILE 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 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 975 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1051 LYS Chi-restraints excluded: chain F residue 1057 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 198 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 216 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN F 483 ASN F 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.169347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114371 restraints weight = 42357.595| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.71 r_work: 0.3077 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19067 Z= 0.129 Angle : 0.578 10.447 25770 Z= 0.298 Chirality : 0.042 0.305 2850 Planarity : 0.004 0.056 3210 Dihedral : 12.467 105.425 2963 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 6.62 % Allowed : 26.63 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2227 helix: 0.78 (0.16), residues: 1148 sheet: -0.52 (0.33), residues: 226 loop : -1.71 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F1032 TYR 0.017 0.001 TYR F 629 PHE 0.024 0.001 PHE F 993 TRP 0.012 0.001 TRP A1406 HIS 0.003 0.001 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.00300 (19053) covalent geometry : angle 0.57718 (25744) SS BOND : bond 0.00367 ( 13) SS BOND : angle 1.24726 ( 26) hydrogen bonds : bond 0.03575 ( 864) hydrogen bonds : angle 3.99707 ( 2510) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 243 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7454 (tt0) REVERT: A 114 GLN cc_start: 0.5949 (tt0) cc_final: 0.5272 (tm-30) REVERT: A 190 PHE cc_start: 0.6731 (t80) cc_final: 0.6372 (m-10) REVERT: A 241 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8552 (ptpt) REVERT: A 308 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: A 483 MET cc_start: 0.2818 (OUTLIER) cc_final: 0.2600 (pp-130) REVERT: A 548 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6245 (tt) REVERT: A 553 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6757 (pp) REVERT: A 851 MET cc_start: 0.2069 (mmm) cc_final: 0.0803 (mmm) REVERT: A 897 ARG cc_start: 0.6117 (ptt180) cc_final: 0.5896 (ptt90) REVERT: A 906 ARG cc_start: 0.4313 (OUTLIER) cc_final: 0.3646 (mtt180) REVERT: A 948 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8204 (mp10) REVERT: A 976 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8153 (mtmt) REVERT: A 983 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8725 (ptp) REVERT: A 1028 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7854 (mm-30) REVERT: A 1051 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8509 (tp) REVERT: A 1096 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6426 (ttm-80) REVERT: A 1105 ASN cc_start: 0.4763 (t0) cc_final: 0.4279 (t0) REVERT: A 1123 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7862 (pp) REVERT: A 1137 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7878 (ttp) REVERT: A 1151 ASP cc_start: 0.7944 (t0) cc_final: 0.7395 (p0) REVERT: A 1175 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6731 (mpp-170) REVERT: A 1201 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5923 (tp30) REVERT: A 1286 MET cc_start: 0.9120 (mtp) cc_final: 0.8878 (mtm) REVERT: A 1371 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.7934 (mp) REVERT: A 1384 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6091 (t80) REVERT: E 113 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.6858 (m-80) REVERT: E 127 MET cc_start: 0.7727 (ttp) cc_final: 0.6647 (tmt) REVERT: E 138 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6345 (ptp-170) REVERT: E 142 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6872 (ptp) REVERT: E 209 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6673 (tp-100) REVERT: E 216 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.5674 (tpt) REVERT: E 219 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5192 (pp20) REVERT: F 205 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8479 (tt) REVERT: F 234 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.6359 (mttt) REVERT: F 286 SER cc_start: 0.8681 (p) cc_final: 0.8474 (t) REVERT: F 307 GLN cc_start: 0.8378 (mt0) cc_final: 0.7912 (mm110) REVERT: F 505 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7891 (ppt-90) REVERT: F 508 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8613 (mt) REVERT: F 545 LYS cc_start: 0.8339 (mttm) cc_final: 0.7983 (mmtt) REVERT: F 674 LYS cc_start: 0.8068 (ptpp) cc_final: 0.7665 (ptmt) REVERT: F 717 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: F 804 TYR cc_start: 0.8352 (m-80) cc_final: 0.7916 (m-80) REVERT: F 975 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6879 (mt0) REVERT: F 1024 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7802 (ttmt) outliers start: 132 outliers final: 69 residues processed: 340 average time/residue: 0.5291 time to fit residues: 206.8254 Evaluate side-chains 326 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 229 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1096 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1201 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 235 ILE 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 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 975 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 82 optimal weight: 9.9990 chunk 149 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN F 424 ASN F 483 ASN F 570 ASN F 644 GLN F 975 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.170800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117687 restraints weight = 41115.923| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.83 r_work: 0.3092 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19067 Z= 0.113 Angle : 0.562 10.353 25770 Z= 0.289 Chirality : 0.042 0.308 2850 Planarity : 0.004 0.055 3210 Dihedral : 12.017 100.965 2959 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.92 % Allowed : 27.13 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.18 (0.18), residues: 2227 helix: 1.00 (0.16), residues: 1145 sheet: -0.44 (0.33), residues: 221 loop : -1.56 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F1032 TYR 0.017 0.001 TYR F 629 PHE 0.026 0.001 PHE A 92 TRP 0.014 0.001 TRP A1406 HIS 0.003 0.001 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.00257 (19053) covalent geometry : angle 0.56076 (25744) SS BOND : bond 0.00380 ( 13) SS BOND : angle 1.13436 ( 26) hydrogen bonds : bond 0.03295 ( 864) hydrogen bonds : angle 3.89698 ( 2510) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 247 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.5935 (tt0) cc_final: 0.5365 (tm-30) REVERT: A 190 PHE cc_start: 0.6624 (t80) cc_final: 0.6271 (m-10) REVERT: A 241 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8472 (ptpt) REVERT: A 308 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: A 479 MET cc_start: 0.6111 (ttp) cc_final: 0.5895 (tmm) REVERT: A 483 MET cc_start: 0.2978 (OUTLIER) cc_final: 0.2724 (pp-130) REVERT: A 548 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6343 (tt) REVERT: A 553 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6753 (pp) REVERT: A 554 ASN cc_start: 0.6216 (t0) cc_final: 0.5280 (p0) REVERT: A 851 MET cc_start: 0.1960 (mmm) cc_final: 0.0791 (mmt) REVERT: A 897 ARG cc_start: 0.6117 (ptt180) cc_final: 0.5874 (ptt90) REVERT: A 906 ARG cc_start: 0.4241 (OUTLIER) cc_final: 0.3597 (mtt180) REVERT: A 938 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8887 (mt) REVERT: A 976 LYS cc_start: 0.8819 (mmpt) cc_final: 0.8192 (mtmt) REVERT: A 983 MET cc_start: 0.8938 (ptm) cc_final: 0.8619 (ptp) REVERT: A 1028 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7869 (mm-30) REVERT: A 1096 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6366 (ttm-80) REVERT: A 1105 ASN cc_start: 0.4670 (t0) cc_final: 0.4177 (t0) REVERT: A 1123 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7821 (pp) REVERT: A 1151 ASP cc_start: 0.7961 (t0) cc_final: 0.7337 (p0) REVERT: A 1175 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6536 (mpp-170) REVERT: A 1201 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5970 (tp30) REVERT: A 1272 LEU cc_start: 0.8402 (tp) cc_final: 0.8024 (mm) REVERT: A 1286 MET cc_start: 0.9083 (mtp) cc_final: 0.8849 (mtm) REVERT: A 1384 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.6224 (t80) REVERT: A 1390 ASP cc_start: 0.6779 (t0) cc_final: 0.6480 (t0) REVERT: E 113 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: E 127 MET cc_start: 0.7650 (ttp) cc_final: 0.6547 (tmt) REVERT: E 142 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6849 (ptp) REVERT: E 189 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6979 (t80) REVERT: E 207 MET cc_start: 0.8313 (mmt) cc_final: 0.7946 (mmm) REVERT: E 216 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5443 (tpt) REVERT: F 59 ASP cc_start: 0.8181 (m-30) cc_final: 0.7962 (m-30) REVERT: F 205 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8474 (tt) REVERT: F 234 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6352 (mttt) REVERT: F 240 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8717 (p) REVERT: F 307 GLN cc_start: 0.8271 (mt0) cc_final: 0.7753 (mm110) REVERT: F 505 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7866 (ppt-90) REVERT: F 508 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8628 (mt) REVERT: F 545 LYS cc_start: 0.8310 (mttm) cc_final: 0.7985 (mmtt) REVERT: F 674 LYS cc_start: 0.8257 (ptpp) cc_final: 0.7793 (ptmt) REVERT: F 717 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: F 804 TYR cc_start: 0.8295 (m-80) cc_final: 0.7850 (m-80) REVERT: F 851 MET cc_start: 0.7232 (ptp) cc_final: 0.6901 (ptm) REVERT: F 1024 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7665 (ttmt) outliers start: 118 outliers final: 52 residues processed: 337 average time/residue: 0.5160 time to fit residues: 199.1555 Evaluate side-chains 307 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 233 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1096 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1201 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1051 LYS Chi-restraints excluded: chain F residue 1057 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 110 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 ASN A 939 GLN E 209 GLN F 483 ASN F 570 ASN F 644 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114944 restraints weight = 37763.138| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.59 r_work: 0.3124 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19067 Z= 0.133 Angle : 0.583 11.524 25770 Z= 0.299 Chirality : 0.042 0.322 2850 Planarity : 0.004 0.053 3210 Dihedral : 11.894 101.548 2951 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.22 % Allowed : 27.98 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.09 (0.18), residues: 2227 helix: 1.07 (0.16), residues: 1137 sheet: -0.51 (0.32), residues: 229 loop : -1.46 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F1032 TYR 0.014 0.001 TYR F 629 PHE 0.020 0.001 PHE F1006 TRP 0.014 0.001 TRP A1406 HIS 0.002 0.001 HIS A1139 Details of bonding type rmsd covalent geometry : bond 0.00314 (19053) covalent geometry : angle 0.58134 (25744) SS BOND : bond 0.00354 ( 13) SS BOND : angle 1.56927 ( 26) hydrogen bonds : bond 0.03494 ( 864) hydrogen bonds : angle 3.94068 ( 2510) Misc. bond : bond 0.00090 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 237 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.5936 (tt0) cc_final: 0.5411 (tm-30) REVERT: A 190 PHE cc_start: 0.6735 (t80) cc_final: 0.6404 (m-10) REVERT: A 241 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8453 (ptpt) REVERT: A 479 MET cc_start: 0.6071 (ttp) cc_final: 0.5850 (tmm) REVERT: A 483 MET cc_start: 0.3082 (OUTLIER) cc_final: 0.2811 (pp-130) REVERT: A 548 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6379 (tt) REVERT: A 553 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6736 (pp) REVERT: A 554 ASN cc_start: 0.6233 (t0) cc_final: 0.5303 (p0) REVERT: A 897 ARG cc_start: 0.6162 (ptt180) cc_final: 0.5957 (ptt90) REVERT: A 906 ARG cc_start: 0.4394 (OUTLIER) cc_final: 0.3735 (mtt180) REVERT: A 948 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: A 976 LYS cc_start: 0.8842 (mmpt) cc_final: 0.8219 (mtmt) REVERT: A 983 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8597 (ptp) REVERT: A 1028 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7801 (mm-30) REVERT: A 1096 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6340 (ttm-80) REVERT: A 1105 ASN cc_start: 0.4736 (t0) cc_final: 0.4263 (t0) REVERT: A 1123 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7832 (pp) REVERT: A 1137 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7800 (ttm) REVERT: A 1151 ASP cc_start: 0.7778 (t0) cc_final: 0.7207 (p0) REVERT: A 1175 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6640 (mpp-170) REVERT: A 1201 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6025 (tp30) REVERT: A 1272 LEU cc_start: 0.8433 (tp) cc_final: 0.8052 (mm) REVERT: A 1286 MET cc_start: 0.9113 (mtp) cc_final: 0.8816 (mtm) REVERT: A 1371 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 1384 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.6269 (t80) REVERT: A 1390 ASP cc_start: 0.6813 (t0) cc_final: 0.6501 (t0) REVERT: E 24 MET cc_start: 0.5887 (tpt) cc_final: 0.5596 (mtt) REVERT: E 113 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: E 127 MET cc_start: 0.7684 (ttp) cc_final: 0.6599 (tmt) REVERT: E 142 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6910 (ptp) REVERT: E 189 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.7031 (t80) REVERT: E 207 MET cc_start: 0.8310 (mmt) cc_final: 0.8071 (mmm) REVERT: E 216 MET cc_start: 0.5865 (OUTLIER) cc_final: 0.5633 (tpt) REVERT: E 219 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.4988 (pp20) REVERT: F 59 ASP cc_start: 0.8197 (m-30) cc_final: 0.7978 (m-30) REVERT: F 205 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8497 (tt) REVERT: F 234 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6369 (mttt) REVERT: F 307 GLN cc_start: 0.8361 (mt0) cc_final: 0.7902 (mm110) REVERT: F 505 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7857 (ppt-90) REVERT: F 508 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8595 (mt) REVERT: F 545 LYS cc_start: 0.8331 (mttm) cc_final: 0.8030 (mmtt) REVERT: F 674 LYS cc_start: 0.8244 (ptpp) cc_final: 0.7788 (ptmt) REVERT: F 717 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: F 804 TYR cc_start: 0.8258 (m-80) cc_final: 0.7909 (m-80) REVERT: F 851 MET cc_start: 0.7252 (ptp) cc_final: 0.7005 (ptm) outliers start: 104 outliers final: 59 residues processed: 312 average time/residue: 0.5082 time to fit residues: 182.0371 Evaluate side-chains 314 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 231 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1096 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1201 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 114 optimal weight: 6.9990 chunk 213 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN F 483 ASN F 570 ASN F 644 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.171241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116506 restraints weight = 39631.173| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.66 r_work: 0.3115 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19067 Z= 0.114 Angle : 0.571 12.330 25770 Z= 0.291 Chirality : 0.042 0.326 2850 Planarity : 0.004 0.053 3210 Dihedral : 11.493 99.198 2948 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.46 % Allowed : 28.54 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.08 (0.18), residues: 2227 helix: 1.26 (0.16), residues: 1131 sheet: -0.44 (0.33), residues: 224 loop : -1.44 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F1032 TYR 0.013 0.001 TYR F 629 PHE 0.026 0.001 PHE A 131 TRP 0.013 0.001 TRP A1406 HIS 0.003 0.001 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.00263 (19053) covalent geometry : angle 0.56942 (25744) SS BOND : bond 0.00309 ( 13) SS BOND : angle 1.43707 ( 26) hydrogen bonds : bond 0.03240 ( 864) hydrogen bonds : angle 3.87412 ( 2510) Misc. bond : bond 0.00075 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 247 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.5782 (tt0) cc_final: 0.5326 (tm-30) REVERT: A 190 PHE cc_start: 0.6835 (t80) cc_final: 0.6362 (m-10) REVERT: A 241 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8514 (ptpt) REVERT: A 308 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8348 (pm20) REVERT: A 479 MET cc_start: 0.6054 (ttp) cc_final: 0.5844 (tmm) REVERT: A 483 MET cc_start: 0.3103 (OUTLIER) cc_final: 0.2826 (pp-130) REVERT: A 548 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6368 (tt) REVERT: A 553 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6737 (pp) REVERT: A 554 ASN cc_start: 0.6476 (t0) cc_final: 0.5667 (p0) REVERT: A 897 ARG cc_start: 0.6104 (ptt180) cc_final: 0.5898 (ptt90) REVERT: A 906 ARG cc_start: 0.4473 (OUTLIER) cc_final: 0.3813 (mtt180) REVERT: A 948 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: A 976 LYS cc_start: 0.8818 (mmpt) cc_final: 0.8279 (mppt) REVERT: A 983 MET cc_start: 0.8855 (ptm) cc_final: 0.8548 (ptp) REVERT: A 1028 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7827 (mm-30) REVERT: A 1096 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6272 (ttm-80) REVERT: A 1105 ASN cc_start: 0.4672 (t0) cc_final: 0.4196 (t0) REVERT: A 1123 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7859 (pp) REVERT: A 1137 MET cc_start: 0.8208 (mtm) cc_final: 0.7824 (ttm) REVERT: A 1151 ASP cc_start: 0.7792 (t0) cc_final: 0.7213 (p0) REVERT: A 1175 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6555 (mpp-170) REVERT: A 1201 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6178 (tp30) REVERT: A 1272 LEU cc_start: 0.8392 (tp) cc_final: 0.8001 (mm) REVERT: A 1371 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.7863 (mp) REVERT: A 1384 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6367 (t80) REVERT: A 1390 ASP cc_start: 0.6778 (t0) cc_final: 0.6510 (t0) REVERT: E 24 MET cc_start: 0.6146 (tpt) cc_final: 0.5724 (mtt) REVERT: E 113 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.6874 (m-80) REVERT: E 127 MET cc_start: 0.7696 (ttp) cc_final: 0.6616 (tmt) REVERT: E 142 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6771 (ptp) REVERT: E 179 SER cc_start: 0.6339 (OUTLIER) cc_final: 0.5680 (m) REVERT: E 219 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5281 (pp20) REVERT: F 59 ASP cc_start: 0.8102 (m-30) cc_final: 0.7881 (m-30) REVERT: F 205 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8418 (tt) REVERT: F 234 LYS cc_start: 0.6708 (OUTLIER) cc_final: 0.6246 (mttt) REVERT: F 307 GLN cc_start: 0.8236 (mt0) cc_final: 0.7712 (mm-40) REVERT: F 505 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7921 (ppt-90) REVERT: F 508 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8657 (mt) REVERT: F 545 LYS cc_start: 0.8316 (mttm) cc_final: 0.8011 (mmtt) REVERT: F 674 LYS cc_start: 0.8265 (ptpp) cc_final: 0.7790 (ptmt) REVERT: F 717 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: F 845 LYS cc_start: 0.6465 (mmpt) cc_final: 0.6257 (mmpt) REVERT: F 1024 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7750 (ttmt) outliers start: 89 outliers final: 53 residues processed: 315 average time/residue: 0.5367 time to fit residues: 193.6356 Evaluate side-chains 309 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1096 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1201 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1051 LYS Chi-restraints excluded: chain F residue 1057 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 93 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 164 optimal weight: 0.0370 chunk 137 optimal weight: 0.0030 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN F 483 ASN F 570 ASN F 644 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.171681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119797 restraints weight = 42420.768| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.05 r_work: 0.3098 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 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 = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19067 Z= 0.111 Angle : 0.570 12.552 25770 Z= 0.290 Chirality : 0.041 0.336 2850 Planarity : 0.004 0.065 3210 Dihedral : 11.307 99.156 2947 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.26 % Allowed : 28.89 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2227 helix: 1.36 (0.16), residues: 1125 sheet: -0.40 (0.33), residues: 222 loop : -1.36 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F1032 TYR 0.013 0.001 TYR F 629 PHE 0.016 0.001 PHE A 112 TRP 0.013 0.001 TRP A1406 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00253 (19053) covalent geometry : angle 0.56850 (25744) SS BOND : bond 0.00290 ( 13) SS BOND : angle 1.35462 ( 26) hydrogen bonds : bond 0.03182 ( 864) hydrogen bonds : angle 3.85861 ( 2510) Misc. bond : bond 0.00075 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 238 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.5768 (tt0) cc_final: 0.5313 (tm-30) REVERT: A 190 PHE cc_start: 0.6776 (t80) cc_final: 0.6339 (m-10) REVERT: A 241 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8574 (ptpt) REVERT: A 247 ARG cc_start: 0.7523 (ttp80) cc_final: 0.6804 (ptm160) REVERT: A 308 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: A 527 LEU cc_start: 0.6726 (mm) cc_final: 0.6270 (tt) REVERT: A 548 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6319 (tt) REVERT: A 553 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6671 (pp) REVERT: A 554 ASN cc_start: 0.6473 (t0) cc_final: 0.5725 (p0) REVERT: A 897 ARG cc_start: 0.6101 (ptt180) cc_final: 0.5887 (ptt90) REVERT: A 906 ARG cc_start: 0.4443 (OUTLIER) cc_final: 0.3795 (mtp180) REVERT: A 948 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: A 976 LYS cc_start: 0.8791 (mmpt) cc_final: 0.8221 (mppt) REVERT: A 983 MET cc_start: 0.8885 (ptm) cc_final: 0.8559 (ptp) REVERT: A 1028 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7753 (mm-30) REVERT: A 1096 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6254 (ttm-80) REVERT: A 1105 ASN cc_start: 0.4668 (t0) cc_final: 0.4209 (t0) REVERT: A 1124 MET cc_start: 0.7845 (mmm) cc_final: 0.7124 (tpp) REVERT: A 1137 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7794 (ttm) REVERT: A 1151 ASP cc_start: 0.7785 (t0) cc_final: 0.7174 (p0) REVERT: A 1175 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6502 (mpp-170) REVERT: A 1201 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.6195 (tp30) REVERT: A 1272 LEU cc_start: 0.8363 (tp) cc_final: 0.7956 (mm) REVERT: A 1371 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.7825 (mp) REVERT: A 1384 PHE cc_start: 0.6689 (OUTLIER) cc_final: 0.6344 (t80) REVERT: A 1390 ASP cc_start: 0.6712 (t0) cc_final: 0.6443 (t0) REVERT: E 24 MET cc_start: 0.6209 (tpt) cc_final: 0.5775 (mtt) REVERT: E 113 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6859 (m-80) REVERT: E 127 MET cc_start: 0.7679 (ttp) cc_final: 0.6580 (tmt) REVERT: E 179 SER cc_start: 0.6483 (OUTLIER) cc_final: 0.5913 (m) REVERT: F 59 ASP cc_start: 0.8144 (m-30) cc_final: 0.7920 (m-30) REVERT: F 205 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8411 (tt) REVERT: F 234 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6218 (mmtt) REVERT: F 307 GLN cc_start: 0.8174 (mt0) cc_final: 0.7706 (mm-40) REVERT: F 442 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8817 (mtpt) REVERT: F 505 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7847 (ppt-90) REVERT: F 508 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8676 (mt) REVERT: F 545 LYS cc_start: 0.8295 (mttm) cc_final: 0.7969 (mmtt) REVERT: F 674 LYS cc_start: 0.8209 (ptpp) cc_final: 0.7774 (ptmt) REVERT: F 717 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: F 851 MET cc_start: 0.7107 (ptp) cc_final: 0.6823 (ptm) REVERT: F 1024 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7681 (ttmt) outliers start: 85 outliers final: 52 residues processed: 306 average time/residue: 0.5306 time to fit residues: 185.5807 Evaluate side-chains 304 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 233 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1096 ARG Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1201 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 215 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 200 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 213 optimal weight: 0.0470 chunk 76 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 217 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN F 483 ASN F 570 ASN F 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.172042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120029 restraints weight = 41314.543| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.74 r_work: 0.3164 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 19067 Z= 0.109 Angle : 0.570 12.127 25770 Z= 0.289 Chirality : 0.041 0.331 2850 Planarity : 0.004 0.062 3210 Dihedral : 11.069 98.818 2943 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.06 % Allowed : 29.09 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 2227 helix: 1.45 (0.16), residues: 1123 sheet: -0.38 (0.33), residues: 222 loop : -1.32 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F1032 TYR 0.010 0.001 TYR A1360 PHE 0.027 0.001 PHE A 92 TRP 0.021 0.001 TRP A1406 HIS 0.003 0.001 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.00247 (19053) covalent geometry : angle 0.56926 (25744) SS BOND : bond 0.00280 ( 13) SS BOND : angle 1.31144 ( 26) hydrogen bonds : bond 0.03130 ( 864) hydrogen bonds : angle 3.82337 ( 2510) Misc. bond : bond 0.00070 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7029.35 seconds wall clock time: 120 minutes 13.77 seconds (7213.77 seconds total)