Starting phenix.real_space_refine on Fri Mar 6 06:21:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlm_22248/03_2026/6xlm_22248.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlm_22248/03_2026/6xlm_22248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xlm_22248/03_2026/6xlm_22248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlm_22248/03_2026/6xlm_22248.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xlm_22248/03_2026/6xlm_22248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlm_22248/03_2026/6xlm_22248.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.100 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 Zn 2 6.06 5 P 40 5.49 5 Mg 1 5.21 5 S 118 5.16 5 C 17594 2.51 5 N 4990 2.21 5 O 5499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.03s 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: 28244 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1793 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain: "B" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1711 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10560 Classifications: {'peptide': 1339} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "D" Number of atoms: 10387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10387 Classifications: {'peptide': 1336} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 2 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2282 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 5, 'TRANS': 272} Chain breaks: 3 Chain: "N" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "R" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 193 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14513 SG CYS D 70 103.224 40.598 87.204 1.00132.18 S ATOM 14527 SG CYS D 72 103.186 37.316 86.584 1.00134.99 S ATOM 14635 SG CYS D 85 105.452 39.414 85.002 1.00135.60 S ATOM 14659 SG CYS D 88 101.783 39.714 84.276 1.00136.35 S ATOM 20347 SG CYS D 814 90.767 106.035 90.888 1.00103.46 S ATOM 20912 SG CYS D 888 88.983 103.035 91.034 1.00107.74 S ATOM 20963 SG CYS D 895 90.275 104.458 93.797 1.00 97.39 S ATOM 20984 SG CYS D 898 87.792 106.194 92.401 1.00100.12 S Time building chain proxies: 5.68, per 1000 atoms: 0.20 Number of scatterers: 28244 At special positions: 0 Unit cell: (141.298, 151.962, 179.955, 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) Zn 2 29.99 S 118 16.00 P 40 15.00 Mg 1 11.99 O 5499 8.00 N 4990 7.00 C 17594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 12 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 53 sheets defined 43.0% alpha, 16.9% beta 15 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.942A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.941A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 212 through 228 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.885A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 4.000A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.511A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.834A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.503A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.712A pdb=" N SER C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.980A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.725A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 481 No H-bonds generated for 'chain 'C' and resid 480 through 481' Processing helix chain 'C' and resid 482 through 486 removed outlier: 4.383A pdb=" N ASP C 485 " --> pdb=" O GLY C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.578A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.772A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 614 removed outlier: 4.143A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 609 through 614' Processing helix chain 'C' and resid 656 through 660 removed outlier: 4.264A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.611A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.678A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 864 removed outlier: 4.154A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 985 through 990 removed outlier: 4.115A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 999 removed outlier: 3.536A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU C 999 " --> pdb=" O ASP C 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 993 through 999' Processing helix chain 'C' and resid 1006 through 1037 removed outlier: 4.064A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.823A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.521A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.533A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1299 through 1310 removed outlier: 3.518A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.586A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.717A pdb=" N HIS D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.569A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.554A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.575A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 removed outlier: 3.584A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.516A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.667A pdb=" N GLU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.566A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.975A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.916A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.591A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.825A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 4.042A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 removed outlier: 3.601A pdb=" N ASN D 489 " --> pdb=" O SER D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.533A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.344A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 removed outlier: 3.676A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.734A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.705A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1242 removed outlier: 7.392A pdb=" N VAL D1226 " --> pdb=" O ARG D1222 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N HIS D1227 " --> pdb=" O LEU D1223 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1243 through 1245 No H-bonds generated for 'chain 'D' and resid 1243 through 1245' Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.735A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.608A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1338 Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.855A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1374 removed outlier: 4.134A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 13 removed outlier: 3.929A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.930A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.622A pdb=" N ALA E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 135 Processing helix chain 'F' and resid 138 through 153 removed outlier: 3.662A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 161 Processing helix chain 'F' and resid 213 through 234 removed outlier: 3.683A pdb=" N ALA F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 236 No H-bonds generated for 'chain 'F' and resid 236 through 236' Processing helix chain 'F' and resid 243 through 257 removed outlier: 3.803A pdb=" N GLU F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 295 removed outlier: 3.762A pdb=" N VAL F 280 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 309 removed outlier: 4.538A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN F 309 " --> pdb=" O LEU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 330 removed outlier: 3.959A pdb=" N LYS F 329 " --> pdb=" O PRO F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 removed outlier: 3.556A pdb=" N GLY F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 383 removed outlier: 3.888A pdb=" N GLU F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 395 removed outlier: 4.312A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.591A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN F 406 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.535A pdb=" N GLY F 424 " --> pdb=" O TYR F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.608A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN F 437 " --> pdb=" O TRP F 433 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG F 441 " --> pdb=" O GLN F 437 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 20 removed outlier: 4.974A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.587A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 20 removed outlier: 6.468A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 111 removed outlier: 4.128A pdb=" N ALA B 138 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N GLY B 108 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N GLU B 136 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 11.208A pdb=" N VAL B 110 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 10.630A pdb=" N THR B 134 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.515A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.156A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.558A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.772A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.688A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.495A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.092A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.576A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.568A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 3.800A pdb=" N VAL C 884 " --> pdb=" O LEU C 918 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.490A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 3.724A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 103 through 112 removed outlier: 6.618A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 159 through 160 removed outlier: 5.421A pdb=" N VAL D 146 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS D 179 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 252 through 253 Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE2, first strand: chain 'D' and resid 706 through 709 Processing sheet with id=AE3, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE4, first strand: chain 'D' and resid 821 through 822 Processing sheet with id=AE5, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.750A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 848 through 849 Processing sheet with id=AE7, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.089A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 991 through 996 removed outlier: 6.464A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 4.346A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1098 through 1100 Processing sheet with id=AF2, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id=AF3, first strand: chain 'D' and resid 1089 through 1090 removed outlier: 3.502A pdb=" N THR D1093 " --> pdb=" O ILE D1090 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1155 through 1156 removed outlier: 6.270A pdb=" N ILE D1155 " --> pdb=" O ILE D1210 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1161 through 1162 Processing sheet with id=AF6, first strand: chain 'D' and resid 1173 through 1176 Processing sheet with id=AF7, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.711A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 162 through 165 1211 hydrogen bonds defined for protein. 3390 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 6.41 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8285 1.33 - 1.45: 4530 1.45 - 1.57: 15647 1.57 - 1.70: 77 1.70 - 1.82: 205 Bond restraints: 28744 Sorted by residual: bond pdb=" N ARG F 374 " pdb=" CA ARG F 374 " ideal model delta sigma weight residual 1.459 1.423 0.036 1.17e-02 7.31e+03 9.54e+00 bond pdb=" CA GLU C 825 " pdb=" C GLU C 825 " ideal model delta sigma weight residual 1.523 1.481 0.041 1.41e-02 5.03e+03 8.50e+00 bond pdb=" CA ASN B 208 " pdb=" C ASN B 208 " ideal model delta sigma weight residual 1.524 1.478 0.046 1.66e-02 3.63e+03 7.65e+00 bond pdb=" CB THR D 890 " pdb=" OG1 THR D 890 " ideal model delta sigma weight residual 1.433 1.392 0.041 1.60e-02 3.91e+03 6.60e+00 bond pdb=" CB THR D 816 " pdb=" OG1 THR D 816 " ideal model delta sigma weight residual 1.433 1.397 0.036 1.60e-02 3.91e+03 5.06e+00 ... (remaining 28739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 37504 1.83 - 3.67: 1329 3.67 - 5.50: 117 5.50 - 7.34: 32 7.34 - 9.17: 3 Bond angle restraints: 38985 Sorted by residual: angle pdb=" CA ASP D 460 " pdb=" CB ASP D 460 " pdb=" CG ASP D 460 " ideal model delta sigma weight residual 112.60 119.01 -6.41 1.00e+00 1.00e+00 4.10e+01 angle pdb=" C LYS D 40 " pdb=" N PRO D 41 " pdb=" CA PRO D 41 " ideal model delta sigma weight residual 119.56 125.10 -5.54 1.01e+00 9.80e-01 3.01e+01 angle pdb=" CA ASP D 462 " pdb=" CB ASP D 462 " pdb=" CG ASP D 462 " ideal model delta sigma weight residual 112.60 117.23 -4.63 1.00e+00 1.00e+00 2.14e+01 angle pdb=" N ARG F 374 " pdb=" CA ARG F 374 " pdb=" C ARG F 374 " ideal model delta sigma weight residual 110.97 106.01 4.96 1.09e+00 8.42e-01 2.07e+01 angle pdb=" N GLY C 597 " pdb=" CA GLY C 597 " pdb=" C GLY C 597 " ideal model delta sigma weight residual 115.59 109.89 5.70 1.32e+00 5.74e-01 1.86e+01 ... (remaining 38980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.22: 16555 24.22 - 48.44: 1030 48.44 - 72.66: 136 72.66 - 96.88: 19 96.88 - 121.09: 4 Dihedral angle restraints: 17744 sinusoidal: 7721 harmonic: 10023 Sorted by residual: dihedral pdb=" CA LYS F 296 " pdb=" C LYS F 296 " pdb=" N MET F 297 " pdb=" CA MET F 297 " ideal model delta harmonic sigma weight residual -180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LYS C 227 " pdb=" C LYS C 227 " pdb=" N VAL C 228 " pdb=" CA VAL C 228 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA SER D 503 " pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta harmonic sigma weight residual -180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 17741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3060 0.046 - 0.091: 1063 0.091 - 0.137: 296 0.137 - 0.182: 31 0.182 - 0.228: 11 Chirality restraints: 4461 Sorted by residual: chirality pdb=" CA HIS D1366 " pdb=" N HIS D1366 " pdb=" C HIS D1366 " pdb=" CB HIS D1366 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ASP D 462 " pdb=" N ASP D 462 " pdb=" C ASP D 462 " pdb=" CB ASP D 462 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE B 183 " pdb=" CA ILE B 183 " pdb=" CG1 ILE B 183 " pdb=" CG2 ILE B 183 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 4458 not shown) Planarity restraints: 4950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 75 " 0.063 2.00e-02 2.50e+03 3.34e-02 2.24e+01 pdb=" CG TYR D 75 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR D 75 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR D 75 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR D 75 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR D 75 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D 75 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 75 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 886 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C VAL D 886 " 0.053 2.00e-02 2.50e+03 pdb=" O VAL D 886 " -0.020 2.00e-02 2.50e+03 pdb=" N SER D 887 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 461 " 0.015 2.00e-02 2.50e+03 1.85e-02 5.96e+00 pdb=" CG PHE D 461 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE D 461 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE D 461 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 461 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 461 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE D 461 " 0.033 2.00e-02 2.50e+03 ... (remaining 4947 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 285 2.56 - 3.14: 23007 3.14 - 3.73: 44617 3.73 - 4.31: 62903 4.31 - 4.90: 104466 Nonbonded interactions: 235278 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 1.972 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 1.995 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.104 2.170 nonbonded pdb=" O ILE C 11 " pdb=" OH TYR C1149 " model vdw 2.197 3.040 nonbonded pdb=" OG SER C 348 " pdb=" OE2 GLU C 349 " model vdw 2.209 3.040 ... (remaining 235273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 159 or resid 169 through 234)) selection = (chain 'B' and resid 5 through 234) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.040 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.880 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.009 0.299 28752 Z= 0.373 Angle : 0.806 17.073 38997 Z= 0.476 Chirality : 0.049 0.228 4461 Planarity : 0.004 0.049 4950 Dihedral : 15.283 121.095 11288 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 0.69 % Favored : 99.28 % Rotamer: Outliers : 0.07 % Allowed : 6.42 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.52 (0.12), residues: 3461 helix: -1.71 (0.12), residues: 1291 sheet: -1.72 (0.22), residues: 426 loop : -1.53 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 374 TYR 0.063 0.002 TYR D 75 PHE 0.033 0.002 PHE D 461 TRP 0.020 0.002 TRP D 115 HIS 0.007 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00786 (28744) covalent geometry : angle 0.79528 (38985) hydrogen bonds : bond 0.15825 ( 1245) hydrogen bonds : angle 7.29512 ( 3470) metal coordination : bond 0.21578 ( 8) metal coordination : angle 7.34790 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 230 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9073 (ttpt) cc_final: 0.8850 (tptp) REVERT: B 200 LYS cc_start: 0.8894 (tttt) cc_final: 0.8579 (ttpt) REVERT: C 130 MET cc_start: 0.9087 (ttm) cc_final: 0.8808 (ttp) REVERT: C 429 MET cc_start: 0.8864 (mtp) cc_final: 0.8545 (mtp) REVERT: C 488 MET cc_start: 0.8488 (mmm) cc_final: 0.8264 (mmm) REVERT: C 515 MET cc_start: 0.8680 (ttp) cc_final: 0.8412 (ttp) REVERT: C 1049 ILE cc_start: 0.9055 (mt) cc_final: 0.8830 (tt) REVERT: C 1131 MET cc_start: 0.8570 (mtt) cc_final: 0.8364 (mtt) REVERT: C 1319 MET cc_start: 0.8707 (tpp) cc_final: 0.8210 (tpp) REVERT: D 197 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8290 (tp30) REVERT: D 237 MET cc_start: 0.9486 (mtm) cc_final: 0.9193 (mtp) REVERT: D 725 MET cc_start: 0.9062 (mtt) cc_final: 0.8802 (mtm) REVERT: D 1095 MET cc_start: 0.6327 (tmm) cc_final: 0.6120 (tmm) REVERT: E 73 GLN cc_start: 0.8337 (mt0) cc_final: 0.8104 (mt0) REVERT: F 322 MET cc_start: 0.7243 (mmm) cc_final: 0.6775 (mpp) REVERT: F 362 ASN cc_start: 0.9142 (m110) cc_final: 0.8941 (m-40) REVERT: F 365 MET cc_start: 0.8986 (ptp) cc_final: 0.8722 (ptp) outliers start: 2 outliers final: 0 residues processed: 232 average time/residue: 0.2367 time to fit residues: 81.4043 Evaluate side-chains 155 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 117 HIS B 103 ASN B 132 HIS B 137 ASN C 41 GLN C 214 ASN C 618 GLN C1134 GLN C1157 GLN C1244 HIS C1257 GLN C1268 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 158 GLN D 274 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 365 GLN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 712 GLN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D1244 GLN D1367 GLN E 72 GLN E 73 GLN F 301 ASN F 323 ASN F 362 ASN F 400 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.100584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.066143 restraints weight = 66988.441| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.05 r_work: 0.2955 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28752 Z= 0.117 Angle : 0.526 8.757 38997 Z= 0.278 Chirality : 0.042 0.159 4461 Planarity : 0.004 0.046 4950 Dihedral : 10.400 73.341 4422 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.87 % Allowed : 9.45 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.06 (0.13), residues: 3461 helix: -0.06 (0.14), residues: 1320 sheet: -1.31 (0.23), residues: 437 loop : -0.97 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 69 TYR 0.023 0.001 TYR F 143 PHE 0.017 0.001 PHE C 545 TRP 0.015 0.001 TRP F 326 HIS 0.007 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00254 (28744) covalent geometry : angle 0.52145 (38985) hydrogen bonds : bond 0.03629 ( 1245) hydrogen bonds : angle 4.93417 ( 3470) metal coordination : bond 0.00949 ( 8) metal coordination : angle 4.06730 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8685 (tttp) REVERT: A 194 GLN cc_start: 0.8566 (pm20) cc_final: 0.8326 (pm20) REVERT: B 75 GLN cc_start: 0.8696 (pp30) cc_final: 0.8444 (pp30) REVERT: B 194 GLN cc_start: 0.8719 (mp10) cc_final: 0.8252 (pp30) REVERT: B 200 LYS cc_start: 0.8714 (tttt) cc_final: 0.8453 (ttpt) REVERT: B 214 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: C 429 MET cc_start: 0.9024 (mtp) cc_final: 0.8650 (mtp) REVERT: C 515 MET cc_start: 0.9027 (ttp) cc_final: 0.8770 (ttp) REVERT: C 654 ASP cc_start: 0.8531 (m-30) cc_final: 0.8320 (m-30) REVERT: C 814 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8108 (t0) REVERT: C 951 MET cc_start: 0.9063 (tpp) cc_final: 0.8842 (tpp) REVERT: C 1028 LYS cc_start: 0.9183 (mtmt) cc_final: 0.8899 (mtmt) REVERT: C 1049 ILE cc_start: 0.9060 (mt) cc_final: 0.8731 (tt) REVERT: C 1131 MET cc_start: 0.8672 (mtt) cc_final: 0.8130 (mtp) REVERT: C 1157 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: C 1319 MET cc_start: 0.8832 (tpp) cc_final: 0.8552 (tpp) REVERT: D 197 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8111 (tp30) REVERT: D 237 MET cc_start: 0.9577 (mtm) cc_final: 0.9289 (mtp) REVERT: D 298 MET cc_start: 0.8796 (mmm) cc_final: 0.8434 (mmp) REVERT: D 329 ASP cc_start: 0.9126 (m-30) cc_final: 0.8542 (m-30) REVERT: D 525 MET cc_start: 0.9291 (ptp) cc_final: 0.9074 (ptp) REVERT: D 725 MET cc_start: 0.9178 (mtt) cc_final: 0.8925 (mtm) REVERT: D 821 MET cc_start: 0.8553 (mmt) cc_final: 0.8285 (mmm) REVERT: E 65 ASP cc_start: 0.9086 (m-30) cc_final: 0.8245 (m-30) REVERT: F 143 TYR cc_start: 0.7554 (m-80) cc_final: 0.7304 (m-80) REVERT: F 362 ASN cc_start: 0.9175 (m-40) cc_final: 0.8692 (t0) outliers start: 26 outliers final: 7 residues processed: 203 average time/residue: 0.1969 time to fit residues: 63.6081 Evaluate side-chains 162 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 974 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 307 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 271 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 117 HIS B 137 ASN C 330 HIS C 620 ASN C 628 HIS C1013 GLN C1209 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 ASN F 331 HIS F 409 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.098535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.065302 restraints weight = 66316.591| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.97 r_work: 0.2932 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 28752 Z= 0.282 Angle : 0.613 12.583 38997 Z= 0.317 Chirality : 0.044 0.149 4461 Planarity : 0.004 0.074 4950 Dihedral : 10.247 73.355 4422 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.31 % Allowed : 12.24 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.69 (0.14), residues: 3461 helix: 0.38 (0.14), residues: 1307 sheet: -1.25 (0.23), residues: 458 loop : -0.82 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1174 TYR 0.022 0.002 TYR D 46 PHE 0.017 0.002 PHE D 437 TRP 0.010 0.001 TRP F 326 HIS 0.010 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00654 (28744) covalent geometry : angle 0.60864 (38985) hydrogen bonds : bond 0.03916 ( 1245) hydrogen bonds : angle 4.90447 ( 3470) metal coordination : bond 0.01540 ( 8) metal coordination : angle 4.18816 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8797 (tptp) REVERT: A 194 GLN cc_start: 0.8593 (pm20) cc_final: 0.8293 (pm20) REVERT: B 147 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8731 (mt0) REVERT: B 200 LYS cc_start: 0.8948 (tttt) cc_final: 0.8725 (ttpp) REVERT: C 239 MET cc_start: 0.5375 (ttp) cc_final: 0.4803 (tmm) REVERT: C 285 ILE cc_start: 0.6094 (tp) cc_final: 0.5603 (tp) REVERT: C 388 LEU cc_start: 0.9024 (mt) cc_final: 0.8720 (tp) REVERT: C 429 MET cc_start: 0.9048 (mtp) cc_final: 0.8706 (mtp) REVERT: C 515 MET cc_start: 0.8997 (ttp) cc_final: 0.8674 (ttp) REVERT: C 768 MET cc_start: 0.8334 (mtm) cc_final: 0.8071 (mtm) REVERT: C 814 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8311 (t0) REVERT: C 951 MET cc_start: 0.9201 (tpp) cc_final: 0.8978 (tpp) REVERT: C 1049 ILE cc_start: 0.9256 (mt) cc_final: 0.8948 (tt) REVERT: C 1131 MET cc_start: 0.8506 (mtt) cc_final: 0.8068 (mtp) REVERT: C 1170 MET cc_start: 0.8949 (tpp) cc_final: 0.8735 (mmm) REVERT: C 1319 MET cc_start: 0.8940 (tpp) cc_final: 0.8675 (tpp) REVERT: D 197 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8238 (tp30) REVERT: D 237 MET cc_start: 0.9581 (mtm) cc_final: 0.9281 (mtp) REVERT: D 298 MET cc_start: 0.8821 (mmm) cc_final: 0.8559 (mmm) REVERT: D 654 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8377 (pt) REVERT: D 725 MET cc_start: 0.9252 (mtt) cc_final: 0.9044 (mtm) REVERT: D 821 MET cc_start: 0.8562 (mmt) cc_final: 0.8339 (mmm) REVERT: E 65 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8244 (m-30) REVERT: F 143 TYR cc_start: 0.7709 (m-80) cc_final: 0.7344 (m-80) REVERT: F 362 ASN cc_start: 0.9149 (m-40) cc_final: 0.8863 (t0) outliers start: 39 outliers final: 18 residues processed: 190 average time/residue: 0.1698 time to fit residues: 53.6192 Evaluate side-chains 170 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 268 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 165 optimal weight: 1.9990 chunk 273 optimal weight: 20.0000 chunk 205 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 277 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS C1013 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.098200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.065150 restraints weight = 66185.863| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.96 r_work: 0.2925 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 28752 Z= 0.280 Angle : 0.608 10.398 38997 Z= 0.314 Chirality : 0.044 0.157 4461 Planarity : 0.004 0.064 4950 Dihedral : 10.214 73.371 4422 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.05 % Allowed : 13.42 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.59 (0.14), residues: 3461 helix: 0.50 (0.14), residues: 1323 sheet: -1.27 (0.23), residues: 467 loop : -0.76 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1174 TYR 0.020 0.002 TYR D 46 PHE 0.015 0.002 PHE D 437 TRP 0.009 0.001 TRP F 326 HIS 0.010 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00650 (28744) covalent geometry : angle 0.60363 (38985) hydrogen bonds : bond 0.03777 ( 1245) hydrogen bonds : angle 4.84612 ( 3470) metal coordination : bond 0.01435 ( 8) metal coordination : angle 4.14105 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 157 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8786 (tptp) REVERT: B 95 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8242 (mtmm) REVERT: B 147 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8702 (mt0) REVERT: B 194 GLN cc_start: 0.8558 (mp10) cc_final: 0.8318 (pp30) REVERT: B 200 LYS cc_start: 0.8969 (tttt) cc_final: 0.8754 (ttpp) REVERT: C 239 MET cc_start: 0.5377 (ttp) cc_final: 0.4713 (tmm) REVERT: C 241 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7907 (pp) REVERT: C 369 MET cc_start: 0.8847 (tmm) cc_final: 0.8601 (tmm) REVERT: C 388 LEU cc_start: 0.9115 (mt) cc_final: 0.8807 (tp) REVERT: C 429 MET cc_start: 0.9058 (mtp) cc_final: 0.8724 (mtp) REVERT: C 515 MET cc_start: 0.8986 (ttp) cc_final: 0.8718 (ttp) REVERT: C 814 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8330 (t0) REVERT: C 951 MET cc_start: 0.9234 (tpp) cc_final: 0.8993 (tpp) REVERT: C 954 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8982 (mtmm) REVERT: C 1028 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8609 (mtmt) REVERT: C 1049 ILE cc_start: 0.9268 (mt) cc_final: 0.8954 (tt) REVERT: C 1131 MET cc_start: 0.8501 (mtt) cc_final: 0.8063 (mtp) REVERT: C 1319 MET cc_start: 0.8870 (tpp) cc_final: 0.8596 (tpp) REVERT: D 180 MET cc_start: 0.7523 (ptm) cc_final: 0.7283 (ptm) REVERT: D 197 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8290 (tp30) REVERT: D 237 MET cc_start: 0.9568 (mtm) cc_final: 0.9292 (mtp) REVERT: D 298 MET cc_start: 0.8868 (mmm) cc_final: 0.8661 (mmm) REVERT: D 525 MET cc_start: 0.9319 (ptp) cc_final: 0.9064 (ptp) REVERT: D 654 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8481 (pt) REVERT: D 725 MET cc_start: 0.9258 (mtt) cc_final: 0.9032 (mtm) REVERT: D 821 MET cc_start: 0.8567 (mmt) cc_final: 0.8324 (mmm) REVERT: D 1189 MET cc_start: 0.9086 (tpp) cc_final: 0.8590 (tpp) REVERT: E 65 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8184 (m-30) REVERT: E 73 GLN cc_start: 0.8224 (mt0) cc_final: 0.7959 (mt0) REVERT: F 143 TYR cc_start: 0.7794 (m-80) cc_final: 0.7500 (m-80) REVERT: F 322 MET cc_start: 0.5789 (mpp) cc_final: 0.5426 (mpp) REVERT: F 362 ASN cc_start: 0.9154 (m-40) cc_final: 0.8626 (t0) outliers start: 61 outliers final: 36 residues processed: 210 average time/residue: 0.1756 time to fit residues: 61.3604 Evaluate side-chains 189 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 246 optimal weight: 2.9990 chunk 292 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 chunk 262 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS B 137 ASN D 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.100546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.067444 restraints weight = 65641.911| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.92 r_work: 0.2986 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28752 Z= 0.131 Angle : 0.509 11.683 38997 Z= 0.265 Chirality : 0.041 0.146 4461 Planarity : 0.004 0.076 4950 Dihedral : 9.919 73.363 4422 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.61 % Allowed : 14.53 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3461 helix: 0.83 (0.15), residues: 1327 sheet: -1.03 (0.24), residues: 449 loop : -0.60 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 69 TYR 0.019 0.001 TYR C1018 PHE 0.011 0.001 PHE F 401 TRP 0.010 0.001 TRP F 326 HIS 0.008 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00299 (28744) covalent geometry : angle 0.50593 (38985) hydrogen bonds : bond 0.03222 ( 1245) hydrogen bonds : angle 4.57086 ( 3470) metal coordination : bond 0.00766 ( 8) metal coordination : angle 2.95614 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8835 (tptp) REVERT: B 76 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: B 95 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8207 (mtmm) REVERT: B 147 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8676 (mt0) REVERT: B 200 LYS cc_start: 0.8987 (tttt) cc_final: 0.8681 (ttpp) REVERT: C 239 MET cc_start: 0.5457 (ttp) cc_final: 0.4691 (tmm) REVERT: C 241 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7728 (pp) REVERT: C 388 LEU cc_start: 0.9115 (mt) cc_final: 0.8811 (tp) REVERT: C 429 MET cc_start: 0.9061 (mtp) cc_final: 0.8735 (mtp) REVERT: C 515 MET cc_start: 0.8894 (ttp) cc_final: 0.8644 (ttp) REVERT: C 814 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8189 (t0) REVERT: C 951 MET cc_start: 0.9204 (tpp) cc_final: 0.8955 (tpp) REVERT: C 1049 ILE cc_start: 0.9257 (mt) cc_final: 0.8920 (tt) REVERT: C 1131 MET cc_start: 0.8635 (mtt) cc_final: 0.8219 (mtp) REVERT: C 1319 MET cc_start: 0.8782 (tpp) cc_final: 0.8562 (tpp) REVERT: D 197 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8185 (tp30) REVERT: D 237 MET cc_start: 0.9567 (mtm) cc_final: 0.9248 (mtp) REVERT: D 525 MET cc_start: 0.9271 (ptp) cc_final: 0.9004 (ptp) REVERT: D 581 MET cc_start: 0.9146 (mtm) cc_final: 0.8857 (mtt) REVERT: D 654 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8479 (pt) REVERT: D 725 MET cc_start: 0.9213 (mtt) cc_final: 0.8988 (mtm) REVERT: D 821 MET cc_start: 0.8547 (mmt) cc_final: 0.8308 (mmm) REVERT: D 1189 MET cc_start: 0.9128 (tpp) cc_final: 0.8802 (tpp) REVERT: E 65 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8229 (m-30) REVERT: F 143 TYR cc_start: 0.7729 (m-80) cc_final: 0.7358 (m-80) REVERT: F 322 MET cc_start: 0.5561 (mpp) cc_final: 0.5237 (mpp) REVERT: F 362 ASN cc_start: 0.9102 (m-40) cc_final: 0.8734 (t0) outliers start: 48 outliers final: 30 residues processed: 199 average time/residue: 0.1752 time to fit residues: 56.9770 Evaluate side-chains 185 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 303 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 308 optimal weight: 7.9990 chunk 160 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 338 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.099697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.066221 restraints weight = 65925.868| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.98 r_work: 0.2954 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28752 Z= 0.186 Angle : 0.540 11.807 38997 Z= 0.278 Chirality : 0.042 0.143 4461 Planarity : 0.004 0.065 4950 Dihedral : 9.809 73.361 4422 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.25 % Allowed : 14.49 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.14), residues: 3461 helix: 0.90 (0.14), residues: 1326 sheet: -0.92 (0.24), residues: 454 loop : -0.49 (0.16), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 69 TYR 0.014 0.001 TYR D 46 PHE 0.012 0.001 PHE D 437 TRP 0.009 0.001 TRP F 326 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00431 (28744) covalent geometry : angle 0.53777 (38985) hydrogen bonds : bond 0.03348 ( 1245) hydrogen bonds : angle 4.56312 ( 3470) metal coordination : bond 0.00969 ( 8) metal coordination : angle 2.89442 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 150 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9073 (ttpt) cc_final: 0.8770 (tptp) REVERT: B 76 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: B 95 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8237 (mtmm) REVERT: B 147 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8703 (mt0) REVERT: B 200 LYS cc_start: 0.8921 (tttt) cc_final: 0.8689 (ttpp) REVERT: C 239 MET cc_start: 0.5413 (ttp) cc_final: 0.4674 (tmm) REVERT: C 241 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7828 (pp) REVERT: C 388 LEU cc_start: 0.9116 (mt) cc_final: 0.8814 (tp) REVERT: C 429 MET cc_start: 0.9061 (mtp) cc_final: 0.8710 (mtp) REVERT: C 515 MET cc_start: 0.9002 (ttp) cc_final: 0.8658 (ttp) REVERT: C 814 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8267 (t0) REVERT: C 951 MET cc_start: 0.9205 (tpp) cc_final: 0.8947 (tpp) REVERT: C 1049 ILE cc_start: 0.9184 (mt) cc_final: 0.8896 (tt) REVERT: C 1131 MET cc_start: 0.8568 (mtt) cc_final: 0.8144 (mtp) REVERT: C 1319 MET cc_start: 0.8817 (tpp) cc_final: 0.8601 (tpp) REVERT: D 197 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8276 (tp30) REVERT: D 237 MET cc_start: 0.9566 (mtm) cc_final: 0.9273 (mtp) REVERT: D 525 MET cc_start: 0.9319 (ptp) cc_final: 0.9035 (ptp) REVERT: D 581 MET cc_start: 0.9169 (mtm) cc_final: 0.8862 (mtt) REVERT: D 654 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8457 (pt) REVERT: D 725 MET cc_start: 0.9221 (mtt) cc_final: 0.8990 (mtm) REVERT: D 821 MET cc_start: 0.8496 (mmt) cc_final: 0.8254 (mmm) REVERT: D 1189 MET cc_start: 0.9132 (tpp) cc_final: 0.8872 (tpp) REVERT: E 65 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: F 143 TYR cc_start: 0.7951 (m-80) cc_final: 0.7605 (m-80) REVERT: F 322 MET cc_start: 0.5783 (mpp) cc_final: 0.5463 (mpp) REVERT: F 342 GLN cc_start: 0.9550 (tp-100) cc_final: 0.9228 (tm-30) REVERT: F 362 ASN cc_start: 0.9118 (m-40) cc_final: 0.8792 (t0) outliers start: 67 outliers final: 46 residues processed: 208 average time/residue: 0.1592 time to fit residues: 55.9747 Evaluate side-chains 197 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 171 optimal weight: 6.9990 chunk 297 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 127 optimal weight: 0.0470 chunk 48 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.099756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.066246 restraints weight = 65390.057| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.97 r_work: 0.2961 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28752 Z= 0.177 Angle : 0.535 12.705 38997 Z= 0.276 Chirality : 0.042 0.144 4461 Planarity : 0.004 0.062 4950 Dihedral : 9.784 73.366 4422 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.29 % Allowed : 14.83 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.02 (0.14), residues: 3461 helix: 0.94 (0.14), residues: 1327 sheet: -0.90 (0.24), residues: 454 loop : -0.44 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 69 TYR 0.021 0.001 TYR C1018 PHE 0.012 0.001 PHE D 437 TRP 0.009 0.001 TRP F 326 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00409 (28744) covalent geometry : angle 0.53323 (38985) hydrogen bonds : bond 0.03313 ( 1245) hydrogen bonds : angle 4.52511 ( 3470) metal coordination : bond 0.00914 ( 8) metal coordination : angle 2.77014 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 151 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9067 (ttpt) cc_final: 0.8755 (tptp) REVERT: B 76 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7482 (pm20) REVERT: B 95 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8313 (mtmm) REVERT: B 147 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8657 (mt0) REVERT: B 200 LYS cc_start: 0.8919 (tttt) cc_final: 0.8586 (ttpp) REVERT: C 239 MET cc_start: 0.5215 (ttp) cc_final: 0.4467 (tmm) REVERT: C 241 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7929 (pp) REVERT: C 388 LEU cc_start: 0.9112 (mt) cc_final: 0.8803 (tp) REVERT: C 429 MET cc_start: 0.9064 (mtp) cc_final: 0.8712 (mtp) REVERT: C 515 MET cc_start: 0.9003 (ttp) cc_final: 0.8676 (ttp) REVERT: C 814 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8229 (t0) REVERT: C 951 MET cc_start: 0.9203 (tpp) cc_final: 0.8942 (tpp) REVERT: C 1049 ILE cc_start: 0.9180 (mt) cc_final: 0.8893 (tt) REVERT: C 1131 MET cc_start: 0.8576 (mtt) cc_final: 0.8149 (mtp) REVERT: C 1319 MET cc_start: 0.8816 (tpp) cc_final: 0.8605 (tpp) REVERT: D 197 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8263 (tp30) REVERT: D 237 MET cc_start: 0.9560 (mtm) cc_final: 0.9265 (mtp) REVERT: D 654 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8455 (pt) REVERT: D 725 MET cc_start: 0.9219 (mtt) cc_final: 0.8984 (mtm) REVERT: D 821 MET cc_start: 0.8496 (mmt) cc_final: 0.8227 (mmm) REVERT: D 1189 MET cc_start: 0.9129 (tpp) cc_final: 0.8890 (tpp) REVERT: E 65 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8257 (m-30) REVERT: F 143 TYR cc_start: 0.7967 (m-80) cc_final: 0.7598 (m-80) REVERT: F 322 MET cc_start: 0.5832 (mpp) cc_final: 0.5526 (mpp) REVERT: F 342 GLN cc_start: 0.9528 (tp-100) cc_final: 0.9198 (tm-30) REVERT: F 362 ASN cc_start: 0.9110 (m-40) cc_final: 0.8764 (t0) outliers start: 68 outliers final: 49 residues processed: 210 average time/residue: 0.1717 time to fit residues: 60.0453 Evaluate side-chains 201 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1338 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 156 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 340 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 277 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 270 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS C 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.096789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.062503 restraints weight = 67309.971| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.96 r_work: 0.2872 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 28752 Z= 0.249 Angle : 0.592 13.206 38997 Z= 0.302 Chirality : 0.044 0.153 4461 Planarity : 0.004 0.061 4950 Dihedral : 9.887 73.377 4422 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.25 % Allowed : 15.50 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.10 (0.14), residues: 3461 helix: 0.89 (0.14), residues: 1326 sheet: -0.93 (0.24), residues: 450 loop : -0.51 (0.16), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 272 TYR 0.021 0.001 TYR D 609 PHE 0.014 0.001 PHE D 437 TRP 0.009 0.001 TRP F 326 HIS 0.007 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00579 (28744) covalent geometry : angle 0.58883 (38985) hydrogen bonds : bond 0.03550 ( 1245) hydrogen bonds : angle 4.62300 ( 3470) metal coordination : bond 0.01208 ( 8) metal coordination : angle 3.26436 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 150 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8908 (mm-30) REVERT: A 125 LYS cc_start: 0.9022 (ttpt) cc_final: 0.8734 (tttp) REVERT: B 76 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: B 95 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8329 (mtmm) REVERT: B 147 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8602 (mt0) REVERT: B 200 LYS cc_start: 0.8837 (tttt) cc_final: 0.8601 (ttpp) REVERT: C 239 MET cc_start: 0.5361 (ttp) cc_final: 0.4584 (tmm) REVERT: C 241 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.7903 (pp) REVERT: C 388 LEU cc_start: 0.9081 (mt) cc_final: 0.8766 (tp) REVERT: C 429 MET cc_start: 0.9044 (mtp) cc_final: 0.8713 (mtp) REVERT: C 639 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8709 (mtmm) REVERT: C 814 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8283 (t0) REVERT: C 951 MET cc_start: 0.9198 (tpp) cc_final: 0.8930 (tpp) REVERT: C 1049 ILE cc_start: 0.9108 (mt) cc_final: 0.8798 (tt) REVERT: C 1131 MET cc_start: 0.8419 (mtt) cc_final: 0.7967 (mtp) REVERT: C 1319 MET cc_start: 0.8928 (tpp) cc_final: 0.8692 (tpp) REVERT: D 197 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8282 (tp30) REVERT: D 237 MET cc_start: 0.9552 (mtm) cc_final: 0.9249 (mtp) REVERT: D 525 MET cc_start: 0.9274 (ptp) cc_final: 0.9070 (ptp) REVERT: D 725 MET cc_start: 0.9198 (mtt) cc_final: 0.8955 (mtm) REVERT: D 821 MET cc_start: 0.8519 (mmt) cc_final: 0.8203 (mmm) REVERT: D 1003 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7654 (tt) REVERT: D 1189 MET cc_start: 0.9136 (tpp) cc_final: 0.8928 (tpp) REVERT: E 65 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8241 (m-30) REVERT: F 143 TYR cc_start: 0.7981 (m-80) cc_final: 0.7619 (m-80) REVERT: F 221 PHE cc_start: 0.6821 (m-80) cc_final: 0.6620 (m-10) REVERT: F 342 GLN cc_start: 0.9449 (tp-100) cc_final: 0.9093 (tm-30) outliers start: 67 outliers final: 52 residues processed: 209 average time/residue: 0.1709 time to fit residues: 59.4429 Evaluate side-chains 205 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1338 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 251 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 324 optimal weight: 30.0000 chunk 255 optimal weight: 7.9990 chunk 308 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 272 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 164 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.099690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.066408 restraints weight = 65833.809| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.84 r_work: 0.2969 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28752 Z= 0.176 Angle : 0.545 12.155 38997 Z= 0.281 Chirality : 0.042 0.177 4461 Planarity : 0.004 0.059 4950 Dihedral : 9.820 73.377 4422 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.08 % Allowed : 16.04 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.03 (0.14), residues: 3461 helix: 0.94 (0.14), residues: 1332 sheet: -0.88 (0.24), residues: 457 loop : -0.48 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 69 TYR 0.024 0.001 TYR D 609 PHE 0.011 0.001 PHE D 141 TRP 0.022 0.001 TRP F 434 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00409 (28744) covalent geometry : angle 0.54330 (38985) hydrogen bonds : bond 0.03321 ( 1245) hydrogen bonds : angle 4.55426 ( 3470) metal coordination : bond 0.00888 ( 8) metal coordination : angle 2.84031 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 146 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8816 (tptp) REVERT: B 76 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: B 95 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8310 (mtmm) REVERT: B 147 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8631 (mt0) REVERT: B 200 LYS cc_start: 0.8976 (tttt) cc_final: 0.8659 (ttpp) REVERT: C 239 MET cc_start: 0.5295 (ttp) cc_final: 0.4614 (tmm) REVERT: C 241 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.7971 (pp) REVERT: C 388 LEU cc_start: 0.9134 (mt) cc_final: 0.8817 (tp) REVERT: C 429 MET cc_start: 0.9066 (mtp) cc_final: 0.8758 (mtp) REVERT: C 515 MET cc_start: 0.8848 (ttp) cc_final: 0.8590 (ttp) REVERT: C 639 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8581 (mtmm) REVERT: C 814 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8206 (t0) REVERT: C 951 MET cc_start: 0.9211 (tpp) cc_final: 0.8949 (tpp) REVERT: C 1049 ILE cc_start: 0.9204 (mt) cc_final: 0.8910 (tt) REVERT: C 1131 MET cc_start: 0.8553 (mtt) cc_final: 0.8119 (mtp) REVERT: C 1319 MET cc_start: 0.8788 (tpp) cc_final: 0.8565 (tpp) REVERT: D 180 MET cc_start: 0.7425 (ptm) cc_final: 0.7052 (ptt) REVERT: D 197 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8272 (tp30) REVERT: D 237 MET cc_start: 0.9550 (mtm) cc_final: 0.9266 (mtp) REVERT: D 725 MET cc_start: 0.9210 (mtt) cc_final: 0.8983 (mtm) REVERT: D 821 MET cc_start: 0.8481 (mmt) cc_final: 0.8237 (mmm) REVERT: D 1003 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7563 (tt) REVERT: D 1189 MET cc_start: 0.9136 (tpp) cc_final: 0.8911 (tpp) REVERT: E 65 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8236 (m-30) REVERT: F 143 TYR cc_start: 0.7960 (m-10) cc_final: 0.7590 (m-80) REVERT: F 342 GLN cc_start: 0.9467 (tp-100) cc_final: 0.9133 (tm-30) outliers start: 62 outliers final: 52 residues processed: 201 average time/residue: 0.1730 time to fit residues: 58.0832 Evaluate side-chains 202 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 143 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1338 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 208 optimal weight: 0.0980 chunk 96 optimal weight: 0.8980 chunk 312 optimal weight: 0.7980 chunk 285 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 221 optimal weight: 0.0010 chunk 35 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.101722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.068638 restraints weight = 65054.563| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.92 r_work: 0.3013 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28752 Z= 0.106 Angle : 0.512 12.326 38997 Z= 0.262 Chirality : 0.041 0.180 4461 Planarity : 0.003 0.058 4950 Dihedral : 9.614 73.378 4422 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.68 % Allowed : 16.58 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.17 (0.15), residues: 3461 helix: 1.16 (0.15), residues: 1331 sheet: -0.79 (0.24), residues: 450 loop : -0.40 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.020 0.001 TYR D 609 PHE 0.015 0.001 PHE F 221 TRP 0.016 0.001 TRP F 434 HIS 0.019 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00239 (28744) covalent geometry : angle 0.51144 (38985) hydrogen bonds : bond 0.02994 ( 1245) hydrogen bonds : angle 4.37432 ( 3470) metal coordination : bond 0.00482 ( 8) metal coordination : angle 1.92949 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9023 (ttpt) cc_final: 0.8789 (tptp) REVERT: B 76 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: B 95 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8284 (mtmm) REVERT: B 147 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8632 (mt0) REVERT: B 200 LYS cc_start: 0.8991 (tttt) cc_final: 0.8675 (ttpp) REVERT: C 239 MET cc_start: 0.5210 (ttp) cc_final: 0.4714 (tmm) REVERT: C 429 MET cc_start: 0.9061 (mtp) cc_final: 0.8820 (mtp) REVERT: C 492 MET cc_start: 0.8062 (ptp) cc_final: 0.7601 (pmm) REVERT: C 639 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8461 (mtmm) REVERT: C 951 MET cc_start: 0.9221 (tpp) cc_final: 0.8958 (tpp) REVERT: C 1049 ILE cc_start: 0.9192 (mt) cc_final: 0.8907 (tt) REVERT: C 1131 MET cc_start: 0.8590 (mtt) cc_final: 0.8299 (mtp) REVERT: D 197 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8256 (tp30) REVERT: D 237 MET cc_start: 0.9591 (mtm) cc_final: 0.9317 (mtp) REVERT: D 725 MET cc_start: 0.9191 (mtt) cc_final: 0.8959 (mtm) REVERT: D 821 MET cc_start: 0.8550 (mmt) cc_final: 0.8292 (mmm) REVERT: D 1189 MET cc_start: 0.9132 (tpp) cc_final: 0.8872 (tpp) REVERT: E 65 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: F 143 TYR cc_start: 0.7930 (m-10) cc_final: 0.7563 (m-80) REVERT: F 277 MET cc_start: 0.8863 (mmm) cc_final: 0.8649 (mmm) REVERT: F 295 CYS cc_start: 0.7767 (m) cc_final: 0.7171 (m) REVERT: F 342 GLN cc_start: 0.9449 (tp-100) cc_final: 0.9118 (tm-30) REVERT: F 425 TYR cc_start: 0.6107 (m-80) cc_final: 0.5852 (m-80) outliers start: 50 outliers final: 34 residues processed: 201 average time/residue: 0.1753 time to fit residues: 58.1758 Evaluate side-chains 186 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1338 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 78 optimal weight: 0.0970 chunk 316 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 109 optimal weight: 0.0020 chunk 271 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN D1350 ASN E 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.101978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068397 restraints weight = 65604.658| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.74 r_work: 0.3031 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28752 Z= 0.106 Angle : 0.511 12.072 38997 Z= 0.260 Chirality : 0.041 0.174 4461 Planarity : 0.004 0.082 4950 Dihedral : 9.543 73.365 4422 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.41 % Allowed : 17.05 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.27 (0.15), residues: 3461 helix: 1.25 (0.15), residues: 1331 sheet: -0.73 (0.24), residues: 457 loop : -0.35 (0.16), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.021 0.001 TYR C1018 PHE 0.015 0.001 PHE C1323 TRP 0.014 0.001 TRP F 434 HIS 0.004 0.001 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00240 (28744) covalent geometry : angle 0.50850 (38985) hydrogen bonds : bond 0.02943 ( 1245) hydrogen bonds : angle 4.32952 ( 3470) metal coordination : bond 0.00605 ( 8) metal coordination : angle 2.83328 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7082.03 seconds wall clock time: 121 minutes 54.80 seconds (7314.80 seconds total)