Starting phenix.real_space_refine on Mon Sep 14 06:50:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xlm_22248/09_2026/6xlm_22248.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlm_22248/09_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_22248/09_2026/6xlm_22248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlm_22248/09_2026/6xlm_22248.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xlm_22248/09_2026/6xlm_22248.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xlm_22248/09_2026/6xlm_22248.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xlm_22248/09_2026/6xlm_22248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlm_22248/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 20 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: 5.53, 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: 2.35 Conformation dependent library (CDL) restraints added in 837.7 milliseconds 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: 3.60 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: 7.12 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=" C4' DT T 8 " pdb=" C3' DT T 8 " ideal model delta sigma weight residual 1.529 1.497 0.032 1.00e-02 1.00e+04 1.04e+01 bond pdb=" C1' DC N 82 " pdb=" N1 DC N 82 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.01e+01 bond pdb=" C3' DG T 5 " pdb=" O3' DG T 5 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.83e+00 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=" C4' DC T 13 " pdb=" C3' DC T 13 " ideal model delta sigma weight residual 1.529 1.498 0.031 1.00e-02 1.00e+04 9.43e+00 ... (remaining 28739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 37430 1.83 - 3.67: 1402 3.67 - 5.50: 118 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=" O4' DC T 9 " pdb=" C4' DC T 9 " pdb=" C3' DC T 9 " ideal model delta sigma weight residual 106.00 102.61 3.39 6.00e-01 2.78e+00 3.19e+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=" O4' DT T 8 " pdb=" C4' DT T 8 " pdb=" C3' DT T 8 " ideal model delta sigma weight residual 106.00 102.72 3.28 6.00e-01 2.78e+00 2.98e+01 angle pdb=" O4' DG N 80 " pdb=" C4' DG N 80 " pdb=" C3' DG N 80 " ideal model delta sigma weight residual 106.00 102.78 3.22 6.00e-01 2.78e+00 2.88e+01 ... (remaining 38980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 15559 18.00 - 36.00: 1617 36.00 - 53.99: 311 53.99 - 71.99: 67 71.99 - 89.99: 18 Dihedral angle restraints: 17572 sinusoidal: 7549 harmonic: 10023 Sorted by residual: dihedral pdb=" O5' A R 9 " pdb=" C5' A R 9 " pdb=" C4' A R 9 " pdb=" C3' A R 9 " ideal model delta sinusoidal sigma weight residual 60.00 9.69 50.31 3 6.40e+00 2.44e-02 4.88e+01 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 ... (remaining 17569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3326 0.053 - 0.105: 909 0.105 - 0.158: 197 0.158 - 0.210: 23 0.210 - 0.263: 6 Chirality restraints: 4461 Sorted by residual: chirality pdb=" P A R 3 " pdb=" OP1 A R 3 " pdb=" OP2 A R 3 " pdb=" O5' A R 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.44 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" P G R 4 " pdb=" OP1 G R 4 " pdb=" OP2 G R 4 " pdb=" O5' G R 4 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" P C R 2 " pdb=" OP1 C R 2 " pdb=" OP2 C R 2 " pdb=" O5' C R 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.23 2.00e-01 2.50e+01 1.38e+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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.720 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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= 0.398 Angle : 0.815 17.073 38997 Z= 0.496 Chirality : 0.051 0.263 4461 Planarity : 0.004 0.049 4950 Dihedral : 15.057 89.988 11116 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/Z covalent geometry : bond 0.00791 / 0.38 (28744) covalent geometry : angle 0.80527 / 0.50 (38985) hydrogen bonds : bond 0.15825 / 10.59 ( 1245) hydrogen bonds : angle 7.29512 / 5.07 ( 3470) metal coordination : bond 0.21578 / 11.93 ( 8) metal coordination : angle 7.34790 / 4.00 ( 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 : 0.974 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: 0.2204 time to fit residues: 76.1428 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 : 0.915 ------------------------------------------------------------------------------- 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... A 23 HIS A 117 HIS B 103 ASN B 132 HIS B 137 ASN C 41 GLN C 214 ASN C 618 GLN C1013 GLN C1134 GLN C1209 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 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 D1350 ASN 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.100861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.067592 restraints weight = 65661.748| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.90 r_work: 0.2990 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28752 Z= 0.138 Angle : 0.584 13.286 38997 Z= 0.311 Chirality : 0.043 0.188 4461 Planarity : 0.004 0.051 4950 Dihedral : 10.061 65.886 4250 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.76 % Favored : 98.21 % Rotamer: Outliers : 0.71 % Allowed : 9.92 % Favored : 89.37 % 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: -1.29 (0.13), residues: 3461 helix: -0.28 (0.14), residues: 1310 sheet: -1.57 (0.21), residues: 458 loop : -1.01 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 69 TYR 0.035 0.002 TYR F 143 PHE 0.015 0.001 PHE C 545 TRP 0.018 0.001 TRP F 326 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (28744) covalent geometry : angle 0.57589 / 0.31 (38985) hydrogen bonds : bond 0.04176 / 2.82 ( 1245) hydrogen bonds : angle 5.25783 / 3.70 ( 3470) metal coordination : bond 0.01508 / 0.75 ( 8) metal coordination : angle 5.42323 / 3.29 ( 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 195 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8779 (tptp) REVERT: A 194 GLN cc_start: 0.8645 (pm20) cc_final: 0.8426 (pm20) REVERT: B 75 GLN cc_start: 0.8548 (pp30) cc_final: 0.8345 (pp30) REVERT: B 194 GLN cc_start: 0.8564 (mp10) cc_final: 0.8163 (pp30) REVERT: B 200 LYS cc_start: 0.8929 (tttt) cc_final: 0.8665 (ttpt) REVERT: C 214 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8686 (t0) REVERT: C 388 LEU cc_start: 0.8872 (mt) cc_final: 0.8624 (tp) REVERT: C 515 MET cc_start: 0.8981 (ttp) cc_final: 0.8726 (ttp) REVERT: C 814 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8085 (t0) REVERT: C 1028 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8857 (mtmt) REVERT: C 1049 ILE cc_start: 0.9180 (mt) cc_final: 0.8941 (tt) REVERT: C 1131 MET cc_start: 0.8687 (mtt) cc_final: 0.8132 (mtp) REVERT: C 1319 MET cc_start: 0.8942 (tpp) cc_final: 0.8627 (tpp) REVERT: D 197 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8184 (tp30) REVERT: D 237 MET cc_start: 0.9579 (mtm) cc_final: 0.9305 (mtp) REVERT: D 298 MET cc_start: 0.8667 (mmm) cc_final: 0.8375 (mmm) REVERT: D 525 MET cc_start: 0.9288 (ptp) cc_final: 0.9084 (ptp) REVERT: D 725 MET cc_start: 0.9216 (mtt) cc_final: 0.8989 (mtm) REVERT: D 821 MET cc_start: 0.8592 (mmt) cc_final: 0.8384 (mmm) REVERT: D 1010 GLN cc_start: 0.8056 (mm110) cc_final: 0.7757 (tm-30) REVERT: E 65 ASP cc_start: 0.8991 (m-30) cc_final: 0.8274 (m-30) REVERT: E 73 GLN cc_start: 0.8219 (mt0) cc_final: 0.8010 (mt0) REVERT: F 143 TYR cc_start: 0.7449 (m-80) cc_final: 0.7202 (m-80) outliers start: 21 outliers final: 6 residues processed: 188 average time/residue: 0.1897 time to fit residues: 57.2424 Evaluate side-chains 158 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 C residue 214 ASN 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 D residue 769 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: 5.9990 chunk 261 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 271 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 117 HIS C 330 HIS C 618 GLN C 620 ASN C 628 HIS ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 ASN D1227 HIS D1244 GLN ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.097847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064647 restraints weight = 66623.178| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.89 r_work: 0.2921 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 28752 Z= 0.345 Angle : 0.675 13.429 38997 Z= 0.351 Chirality : 0.047 0.207 4461 Planarity : 0.005 0.045 4950 Dihedral : 10.082 64.224 4250 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.55 % Allowed : 12.17 % Favored : 86.28 % 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: -1.03 (0.14), residues: 3461 helix: 0.03 (0.14), residues: 1307 sheet: -1.47 (0.22), residues: 469 loop : -0.93 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1174 TYR 0.025 0.002 TYR F 430 PHE 0.016 0.002 PHE D 437 TRP 0.013 0.002 TRP F 326 HIS 0.023 0.002 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.34 (28744) covalent geometry : angle 0.66904 / 0.35 (38985) hydrogen bonds : bond 0.04322 / 2.95 ( 1245) hydrogen bonds : angle 5.17106 / 3.64 ( 3470) metal coordination : bond 0.01969 / 1.09 ( 8) metal coordination : angle 5.09408 / 3.08 ( 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 203 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8795 (tptp) REVERT: A 194 GLN cc_start: 0.8623 (pm20) cc_final: 0.8354 (pm20) REVERT: B 75 GLN cc_start: 0.8753 (pp30) cc_final: 0.8538 (pp30) REVERT: B 200 LYS cc_start: 0.8955 (tttt) cc_final: 0.8724 (ttpp) REVERT: C 388 LEU cc_start: 0.8912 (mt) cc_final: 0.8622 (tp) REVERT: C 429 MET cc_start: 0.9053 (mtt) cc_final: 0.8837 (mtt) REVERT: C 515 MET cc_start: 0.9018 (ttp) cc_final: 0.8715 (ttp) REVERT: C 615 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8395 (p) REVERT: C 805 MET cc_start: 0.8921 (ptm) cc_final: 0.8617 (ptm) REVERT: C 814 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8305 (t0) REVERT: C 954 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9182 (mtmm) REVERT: C 1028 LYS cc_start: 0.9032 (mtmt) cc_final: 0.8799 (mtmt) REVERT: C 1049 ILE cc_start: 0.9188 (mt) cc_final: 0.8950 (tt) REVERT: C 1319 MET cc_start: 0.8946 (tpp) cc_final: 0.8656 (tpp) REVERT: D 197 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8436 (tp30) REVERT: D 237 MET cc_start: 0.9581 (mtm) cc_final: 0.9327 (mtp) REVERT: D 725 MET cc_start: 0.9272 (mtt) cc_final: 0.9058 (mtm) REVERT: D 1010 GLN cc_start: 0.8141 (mm110) cc_final: 0.7760 (tm-30) REVERT: D 1095 MET cc_start: 0.6415 (tmm) cc_final: 0.6128 (tmm) REVERT: E 61 ASN cc_start: 0.8840 (t0) cc_final: 0.8325 (t0) REVERT: E 65 ASP cc_start: 0.9054 (m-30) cc_final: 0.8193 (m-30) REVERT: F 143 TYR cc_start: 0.7398 (m-80) cc_final: 0.7138 (m-80) outliers start: 46 outliers final: 25 residues processed: 196 average time/residue: 0.1657 time to fit residues: 54.1648 Evaluate side-chains 177 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 92 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 954 LYS 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 769 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain F residue 142 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 165 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 340 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 189 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 chunk 277 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 HIS B 137 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 ASN 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 = 0.098184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.065160 restraints weight = 66174.992| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.00 r_work: 0.2920 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 28752 Z= 0.276 Angle : 0.618 12.929 38997 Z= 0.321 Chirality : 0.045 0.207 4461 Planarity : 0.004 0.045 4950 Dihedral : 10.044 63.904 4250 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.65 % Allowed : 14.19 % Favored : 84.16 % 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: -0.80 (0.14), residues: 3461 helix: 0.27 (0.14), residues: 1305 sheet: -1.39 (0.23), residues: 461 loop : -0.82 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D1174 TYR 0.025 0.002 TYR D 46 PHE 0.015 0.002 PHE D 437 TRP 0.010 0.001 TRP F 326 HIS 0.005 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.28 (28744) covalent geometry : angle 0.61215 / 0.32 (38985) hydrogen bonds : bond 0.03974 / 2.70 ( 1245) hydrogen bonds : angle 5.00679 / 3.53 ( 3470) metal coordination : bond 0.01352 / 0.72 ( 8) metal coordination : angle 4.74651 / 2.90 ( 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 204 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9081 (ttpt) cc_final: 0.8788 (tptp) REVERT: A 194 GLN cc_start: 0.8592 (pm20) cc_final: 0.8321 (pm20) REVERT: B 147 GLN cc_start: 0.8931 (mt0) cc_final: 0.8654 (mt0) REVERT: B 200 LYS cc_start: 0.8949 (tttt) cc_final: 0.8726 (ttpp) REVERT: C 369 MET cc_start: 0.8968 (tmm) cc_final: 0.8618 (tmm) REVERT: C 388 LEU cc_start: 0.9007 (mt) cc_final: 0.8717 (tp) REVERT: C 488 MET cc_start: 0.8537 (mmm) cc_final: 0.8302 (mmm) REVERT: C 515 MET cc_start: 0.9008 (ttp) cc_final: 0.8674 (ttp) REVERT: C 615 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8391 (p) REVERT: C 805 MET cc_start: 0.8955 (ptm) cc_final: 0.8694 (ptm) REVERT: C 814 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8296 (t0) REVERT: C 954 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9132 (mtmm) REVERT: C 1028 LYS cc_start: 0.9057 (mtmt) cc_final: 0.8829 (mtmt) REVERT: C 1049 ILE cc_start: 0.9252 (mt) cc_final: 0.8947 (tt) REVERT: C 1319 MET cc_start: 0.8937 (tpp) cc_final: 0.8690 (tpp) REVERT: D 197 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8311 (tp30) REVERT: D 237 MET cc_start: 0.9580 (mtm) cc_final: 0.9312 (mtp) REVERT: D 725 MET cc_start: 0.9234 (mtt) cc_final: 0.9026 (mtm) REVERT: D 1010 GLN cc_start: 0.8169 (mm110) cc_final: 0.7798 (tm-30) REVERT: E 35 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8280 (mmtp) REVERT: E 61 ASN cc_start: 0.8833 (t0) cc_final: 0.8315 (t0) REVERT: E 65 ASP cc_start: 0.9055 (m-30) cc_final: 0.8189 (m-30) REVERT: F 143 TYR cc_start: 0.7520 (m-80) cc_final: 0.7315 (m-80) outliers start: 49 outliers final: 27 residues processed: 195 average time/residue: 0.1658 time to fit residues: 53.6146 Evaluate side-chains 179 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 183 ILE Chi-restraints excluded: chain C residue 122 VAL 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 615 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 768 MET 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 D residue 708 ASN 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 1163 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1366 HIS 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: 0.7980 chunk 292 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 262 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN C 618 GLN D 45 ASN F 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.100533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.067109 restraints weight = 65503.250| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.99 r_work: 0.2975 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28752 Z= 0.122 Angle : 0.538 14.765 38997 Z= 0.281 Chirality : 0.042 0.197 4461 Planarity : 0.004 0.079 4950 Dihedral : 9.729 64.246 4250 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.51 % Allowed : 14.69 % Favored : 83.79 % 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: -0.43 (0.14), residues: 3461 helix: 0.61 (0.14), residues: 1313 sheet: -1.28 (0.23), residues: 446 loop : -0.63 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1174 TYR 0.024 0.001 TYR D 46 PHE 0.017 0.001 PHE F 427 TRP 0.011 0.001 TRP F 326 HIS 0.005 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (28744) covalent geometry : angle 0.53361 / 0.28 (38985) hydrogen bonds : bond 0.03468 / 2.36 ( 1245) hydrogen bonds : angle 4.72712 / 3.34 ( 3470) metal coordination : bond 0.00732 / 0.37 ( 8) metal coordination : angle 3.93776 / 2.43 ( 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 206 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8851 (tttp) REVERT: A 194 GLN cc_start: 0.8582 (pm20) cc_final: 0.8340 (pm20) REVERT: B 75 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8350 (pp30) REVERT: B 147 GLN cc_start: 0.8979 (mt0) cc_final: 0.8705 (mt0) REVERT: C 130 MET cc_start: 0.9176 (ttm) cc_final: 0.8762 (ttm) REVERT: C 241 LEU cc_start: 0.8509 (tt) cc_final: 0.7816 (pp) REVERT: C 378 ARG cc_start: 0.7676 (ttt-90) cc_final: 0.7462 (tpt-90) REVERT: C 388 LEU cc_start: 0.9011 (mt) cc_final: 0.8702 (tp) REVERT: C 515 MET cc_start: 0.8915 (ttp) cc_final: 0.8613 (ttp) REVERT: C 615 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8323 (p) REVERT: C 805 MET cc_start: 0.8976 (ptm) cc_final: 0.8700 (ptm) REVERT: C 814 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8135 (t0) REVERT: C 1028 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8828 (mtmt) REVERT: C 1049 ILE cc_start: 0.9219 (mt) cc_final: 0.8920 (tt) REVERT: C 1319 MET cc_start: 0.8841 (tpp) cc_final: 0.8587 (tpp) REVERT: D 197 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8173 (tp30) REVERT: D 237 MET cc_start: 0.9592 (mtm) cc_final: 0.9334 (mtp) REVERT: D 725 MET cc_start: 0.9203 (mtt) cc_final: 0.8973 (mtm) REVERT: D 1010 GLN cc_start: 0.8181 (mm110) cc_final: 0.7930 (tm-30) REVERT: E 35 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8267 (mmtp) REVERT: E 65 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8307 (m-30) REVERT: F 143 TYR cc_start: 0.7474 (m-10) cc_final: 0.7248 (m-80) REVERT: F 430 TYR cc_start: 0.6636 (t80) cc_final: 0.6412 (t80) outliers start: 45 outliers final: 25 residues processed: 197 average time/residue: 0.1720 time to fit residues: 55.7175 Evaluate side-chains 182 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS 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 194 GLN Chi-restraints excluded: chain C residue 338 THR 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 615 VAL Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1338 GLU Chi-restraints excluded: chain D residue 573 THR 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 1163 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 ASP 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: 7.9990 chunk 308 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 289 optimal weight: 4.9990 chunk 338 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.099116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.066088 restraints weight = 65953.143| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.95 r_work: 0.2946 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28752 Z= 0.225 Angle : 0.576 10.782 38997 Z= 0.298 Chirality : 0.043 0.221 4461 Planarity : 0.004 0.067 4950 Dihedral : 9.639 63.853 4250 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.15 % Allowed : 15.06 % Favored : 82.78 % 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: -0.37 (0.14), residues: 3461 helix: 0.66 (0.14), residues: 1318 sheet: -1.21 (0.23), residues: 459 loop : -0.61 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 12 TYR 0.021 0.001 TYR D 46 PHE 0.012 0.001 PHE D 437 TRP 0.010 0.001 TRP F 326 HIS 0.005 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (28744) covalent geometry : angle 0.57272 / 0.30 (38985) hydrogen bonds : bond 0.03607 / 2.46 ( 1245) hydrogen bonds : angle 4.73777 / 3.34 ( 3470) metal coordination : bond 0.01145 / 0.60 ( 8) metal coordination : angle 3.75709 / 2.30 ( 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 224 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 160 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9066 (ttpt) cc_final: 0.8813 (tttp) REVERT: B 147 GLN cc_start: 0.8968 (mt0) cc_final: 0.8698 (mt0) REVERT: C 239 MET cc_start: 0.5355 (ttp) cc_final: 0.5045 (ttp) REVERT: C 241 LEU cc_start: 0.8491 (tt) cc_final: 0.7873 (pp) REVERT: C 388 LEU cc_start: 0.9059 (mt) cc_final: 0.8748 (tp) REVERT: C 515 MET cc_start: 0.8982 (ttp) cc_final: 0.8726 (ttp) REVERT: C 615 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8352 (p) REVERT: C 805 MET cc_start: 0.8968 (ptm) cc_final: 0.8677 (ptm) REVERT: C 814 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8269 (t0) REVERT: C 1028 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8692 (mtmt) REVERT: C 1049 ILE cc_start: 0.9250 (mt) cc_final: 0.8931 (tt) REVERT: C 1319 MET cc_start: 0.8843 (tpp) cc_final: 0.8612 (tpp) REVERT: D 197 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8257 (tp30) REVERT: D 237 MET cc_start: 0.9591 (mtm) cc_final: 0.9329 (mtp) REVERT: D 654 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8540 (pt) REVERT: D 725 MET cc_start: 0.9250 (mtt) cc_final: 0.9018 (mtm) REVERT: D 1010 GLN cc_start: 0.8228 (mm110) cc_final: 0.7927 (tm-30) REVERT: D 1095 MET cc_start: 0.6430 (tmm) cc_final: 0.6212 (tmm) REVERT: E 35 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8264 (mmtp) REVERT: E 65 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: F 143 TYR cc_start: 0.7501 (m-10) cc_final: 0.7257 (m-80) REVERT: F 430 TYR cc_start: 0.6649 (t80) cc_final: 0.6400 (t80) outliers start: 64 outliers final: 40 residues processed: 214 average time/residue: 0.1699 time to fit residues: 60.0229 Evaluate side-chains 195 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS 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 232 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 338 THR 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 615 VAL Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1131 MET 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 192 MET 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 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 38 LEU 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: 5.9990 chunk 297 optimal weight: 3.9990 chunk 165 optimal weight: 0.0000 chunk 21 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 229 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 237 optimal weight: 0.9980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 331 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.100485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.067233 restraints weight = 65157.786| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.99 r_work: 0.2977 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28752 Z= 0.125 Angle : 0.535 12.598 38997 Z= 0.278 Chirality : 0.042 0.197 4461 Planarity : 0.004 0.062 4950 Dihedral : 9.484 64.363 4250 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.82 % Allowed : 15.80 % Favored : 82.38 % 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: -0.22 (0.14), residues: 3461 helix: 0.80 (0.14), residues: 1319 sheet: -1.14 (0.24), residues: 454 loop : -0.53 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 69 TYR 0.021 0.001 TYR C1018 PHE 0.011 0.001 PHE F 401 TRP 0.010 0.001 TRP F 326 HIS 0.004 0.001 HIS D 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (28744) covalent geometry : angle 0.52881 / 0.28 (38985) hydrogen bonds : bond 0.03370 / 2.30 ( 1245) hydrogen bonds : angle 4.60683 / 3.25 ( 3470) metal coordination : bond 0.01405 / 0.78 ( 8) metal coordination : angle 4.57181 / 2.68 ( 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 209 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 155 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9072 (ttpt) cc_final: 0.8784 (tptp) REVERT: B 147 GLN cc_start: 0.9008 (mt0) cc_final: 0.8700 (mt0) REVERT: C 130 MET cc_start: 0.9177 (ttm) cc_final: 0.8770 (ttm) REVERT: C 239 MET cc_start: 0.5303 (ttp) cc_final: 0.4985 (ttp) REVERT: C 241 LEU cc_start: 0.8534 (tt) cc_final: 0.7975 (pp) REVERT: C 515 MET cc_start: 0.8964 (ttp) cc_final: 0.8657 (ttp) REVERT: C 805 MET cc_start: 0.9012 (ptm) cc_final: 0.8714 (ptm) REVERT: C 814 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8181 (t0) REVERT: C 1024 GLU cc_start: 0.8780 (pp20) cc_final: 0.8509 (pp20) REVERT: C 1028 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8451 (mtmt) REVERT: C 1049 ILE cc_start: 0.9223 (mt) cc_final: 0.8902 (tt) REVERT: C 1319 MET cc_start: 0.8801 (tpp) cc_final: 0.8574 (tpp) REVERT: D 197 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8169 (tp30) REVERT: D 237 MET cc_start: 0.9599 (mtm) cc_final: 0.9316 (mtp) REVERT: D 654 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8486 (pt) REVERT: D 725 MET cc_start: 0.9225 (mtt) cc_final: 0.8985 (mtm) REVERT: D 1010 GLN cc_start: 0.8217 (mm110) cc_final: 0.7876 (tm-30) REVERT: E 61 ASN cc_start: 0.8821 (t0) cc_final: 0.8272 (t0) REVERT: E 65 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8193 (m-30) REVERT: F 143 TYR cc_start: 0.7637 (m-10) cc_final: 0.7316 (m-80) REVERT: F 430 TYR cc_start: 0.6673 (t80) cc_final: 0.6467 (t80) outliers start: 54 outliers final: 38 residues processed: 202 average time/residue: 0.1816 time to fit residues: 61.4406 Evaluate side-chains 188 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS 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 C residue 122 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 338 THR 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 814 ASP Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1255 THR 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 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 982 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 38 LEU 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: 1.9990 chunk 44 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 340 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 277 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 270 optimal weight: 20.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN C 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.099080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.065806 restraints weight = 65945.482| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.82 r_work: 0.2957 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28752 Z= 0.228 Angle : 0.588 12.715 38997 Z= 0.301 Chirality : 0.044 0.187 4461 Planarity : 0.004 0.060 4950 Dihedral : 9.459 63.987 4250 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.19 % Allowed : 15.77 % Favored : 82.04 % 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: 0.79 (0.14), residues: 1320 sheet: -1.07 (0.24), residues: 457 loop : -0.53 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 12 TYR 0.020 0.001 TYR D 609 PHE 0.014 0.001 PHE D 437 TRP 0.010 0.001 TRP F 326 HIS 0.005 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (28744) covalent geometry : angle 0.58289 / 0.30 (38985) hydrogen bonds : bond 0.03563 / 2.44 ( 1245) hydrogen bonds : angle 4.66054 / 3.28 ( 3470) metal coordination : bond 0.01415 / 0.86 ( 8) metal coordination : angle 4.63868 / 2.65 ( 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 214 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 149 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8841 (tttp) REVERT: B 147 GLN cc_start: 0.8935 (mt0) cc_final: 0.8646 (mt0) REVERT: C 241 LEU cc_start: 0.8461 (tt) cc_final: 0.8103 (pp) REVERT: C 515 MET cc_start: 0.8970 (ttp) cc_final: 0.8697 (ttp) REVERT: C 805 MET cc_start: 0.9068 (ptm) cc_final: 0.8723 (ptm) REVERT: C 814 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8308 (t0) REVERT: C 1049 ILE cc_start: 0.9249 (mt) cc_final: 0.8922 (tt) REVERT: C 1157 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8521 (pt0) REVERT: C 1319 MET cc_start: 0.8786 (tpp) cc_final: 0.8568 (tpp) REVERT: D 197 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8281 (tp30) REVERT: D 237 MET cc_start: 0.9589 (mtm) cc_final: 0.9329 (mtp) REVERT: D 654 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8545 (pt) REVERT: D 725 MET cc_start: 0.9244 (mtt) cc_final: 0.9010 (mtm) REVERT: D 903 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8567 (mm) REVERT: D 1010 GLN cc_start: 0.8266 (mm110) cc_final: 0.7880 (tm-30) REVERT: E 61 ASN cc_start: 0.8836 (t0) cc_final: 0.8296 (t0) REVERT: E 65 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8183 (m-30) REVERT: F 143 TYR cc_start: 0.7636 (m-10) cc_final: 0.7316 (m-80) outliers start: 65 outliers final: 47 residues processed: 205 average time/residue: 0.1724 time to fit residues: 59.9846 Evaluate side-chains 196 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS 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 232 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 338 THR 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 1157 GLN 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 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 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 903 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 1002 VAL 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 38 LEU 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: 0.6980 chunk 80 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 chunk 255 optimal weight: 7.9990 chunk 308 optimal weight: 2.9990 chunk 282 optimal weight: 8.9990 chunk 272 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 256 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.099434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.066113 restraints weight = 65806.895| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.87 r_work: 0.2959 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28752 Z= 0.188 Angle : 0.571 12.287 38997 Z= 0.293 Chirality : 0.043 0.188 4461 Planarity : 0.004 0.059 4950 Dihedral : 9.407 63.958 4250 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.98 % Allowed : 16.17 % Favored : 81.84 % 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: -0.16 (0.14), residues: 3461 helix: 0.83 (0.14), residues: 1319 sheet: -1.07 (0.24), residues: 447 loop : -0.50 (0.16), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.016 0.001 TYR D 609 PHE 0.012 0.001 PHE D 437 TRP 0.010 0.001 TRP F 326 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (28744) covalent geometry : angle 0.56665 / 0.29 (38985) hydrogen bonds : bond 0.03457 / 2.37 ( 1245) hydrogen bonds : angle 4.62898 / 3.26 ( 3470) metal coordination : bond 0.01122 / 0.66 ( 8) metal coordination : angle 4.20907 / 2.44 ( 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 206 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.8846 (mm-30) REVERT: A 125 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8809 (tptp) REVERT: B 147 GLN cc_start: 0.8945 (mt0) cc_final: 0.8653 (mt0) REVERT: C 515 MET cc_start: 0.8962 (ttp) cc_final: 0.8696 (ttp) REVERT: C 805 MET cc_start: 0.9066 (ptm) cc_final: 0.8731 (ptm) REVERT: C 814 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8263 (t0) REVERT: C 1049 ILE cc_start: 0.9250 (mt) cc_final: 0.8913 (tt) REVERT: C 1319 MET cc_start: 0.8788 (tpp) cc_final: 0.8571 (tpp) REVERT: D 197 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8228 (tp30) REVERT: D 237 MET cc_start: 0.9587 (mtm) cc_final: 0.9322 (mtp) REVERT: D 625 MET cc_start: 0.9155 (ttp) cc_final: 0.8919 (ttp) REVERT: D 654 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8530 (pt) REVERT: D 725 MET cc_start: 0.9237 (mtt) cc_final: 0.9007 (mtm) REVERT: D 1010 GLN cc_start: 0.8163 (mm110) cc_final: 0.7842 (tm-30) REVERT: E 61 ASN cc_start: 0.8832 (t0) cc_final: 0.8278 (t0) REVERT: E 65 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8172 (m-30) REVERT: F 143 TYR cc_start: 0.7644 (m-10) cc_final: 0.7306 (m-80) outliers start: 59 outliers final: 47 residues processed: 199 average time/residue: 0.1661 time to fit residues: 56.5048 Evaluate side-chains 195 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain A residue 160 HIS 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 183 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 338 THR 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 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 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 1002 VAL 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 38 LEU 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: 4.9990 chunk 12 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 chunk 312 optimal weight: 4.9990 chunk 285 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 221 optimal weight: 0.0060 chunk 35 optimal weight: 0.1980 chunk 170 optimal weight: 4.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.100432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.067285 restraints weight = 65234.477| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.88 r_work: 0.2985 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28752 Z= 0.135 Angle : 0.552 13.108 38997 Z= 0.284 Chirality : 0.042 0.219 4461 Planarity : 0.004 0.057 4950 Dihedral : 9.292 64.216 4250 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.78 % Allowed : 16.31 % Favored : 81.91 % 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: 0.90 (0.14), residues: 1331 sheet: -1.01 (0.24), residues: 452 loop : -0.50 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.016 0.001 TYR D 609 PHE 0.010 0.001 PHE F 401 TRP 0.011 0.001 TRP F 326 HIS 0.004 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (28744) covalent geometry : angle 0.54844 / 0.28 (38985) hydrogen bonds : bond 0.03287 / 2.25 ( 1245) hydrogen bonds : angle 4.55640 / 3.21 ( 3470) metal coordination : bond 0.00842 / 0.49 ( 8) metal coordination : angle 3.70124 / 2.16 ( 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 206 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.9063 (ttpt) cc_final: 0.8791 (tptp) REVERT: B 147 GLN cc_start: 0.8947 (mt0) cc_final: 0.8660 (mt0) REVERT: C 429 MET cc_start: 0.8949 (mtp) cc_final: 0.8655 (mtt) REVERT: C 515 MET cc_start: 0.8920 (ttp) cc_final: 0.8614 (ttp) REVERT: C 805 MET cc_start: 0.8965 (ptm) cc_final: 0.8696 (ptm) REVERT: C 814 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8226 (t0) REVERT: C 1049 ILE cc_start: 0.9197 (mt) cc_final: 0.8907 (tt) REVERT: C 1319 MET cc_start: 0.8767 (tpp) cc_final: 0.8537 (tpp) REVERT: D 197 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8198 (tp30) REVERT: D 237 MET cc_start: 0.9573 (mtm) cc_final: 0.9306 (mtp) REVERT: D 581 MET cc_start: 0.9141 (mtm) cc_final: 0.8843 (mtt) REVERT: D 625 MET cc_start: 0.9137 (ttp) cc_final: 0.8927 (ttp) REVERT: D 654 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8548 (pt) REVERT: D 725 MET cc_start: 0.9227 (mtt) cc_final: 0.8995 (mtm) REVERT: D 1010 GLN cc_start: 0.8157 (mm110) cc_final: 0.7812 (tm-30) REVERT: E 61 ASN cc_start: 0.8824 (t0) cc_final: 0.8276 (t0) REVERT: E 65 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8188 (m-30) REVERT: F 143 TYR cc_start: 0.7642 (m-10) cc_final: 0.7266 (m-80) REVERT: F 276 MET cc_start: 0.8743 (ptp) cc_final: 0.8503 (ptp) outliers start: 53 outliers final: 45 residues processed: 201 average time/residue: 0.1625 time to fit residues: 55.5042 Evaluate side-chains 196 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS 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 C residue 122 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 338 THR 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 624 ILE 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 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 38 LEU 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 78 optimal weight: 0.0870 chunk 316 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1013 GLN D 424 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.098567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065409 restraints weight = 65925.832| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.88 r_work: 0.2938 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 28752 Z= 0.274 Angle : 0.629 13.481 38997 Z= 0.320 Chirality : 0.045 0.189 4461 Planarity : 0.004 0.061 4950 Dihedral : 9.387 63.233 4250 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.92 % Allowed : 16.27 % Favored : 81.81 % 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: -0.18 (0.14), residues: 3461 helix: 0.82 (0.14), residues: 1323 sheet: -1.01 (0.24), residues: 456 loop : -0.54 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 69 TYR 0.020 0.002 TYR A 185 PHE 0.016 0.002 PHE D 437 TRP 0.010 0.001 TRP F 326 HIS 0.006 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.27 (28744) covalent geometry : angle 0.62428 / 0.32 (38985) hydrogen bonds : bond 0.03656 / 2.50 ( 1245) hydrogen bonds : angle 4.69046 / 3.29 ( 3470) metal coordination : bond 0.01532 / 0.89 ( 8) metal coordination : angle 4.23142 / 2.42 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6795.84 seconds wall clock time: 117 minutes 17.55 seconds (7037.55 seconds total)