Starting phenix.real_space_refine on Thu Oct 29 07:58:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xll_22247/10_2026/6xll_22247.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xll_22247/10_2026/6xll_22247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6xll_22247/10_2026/6xll_22247.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xll_22247/10_2026/6xll_22247.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xll_22247/10_2026/6xll_22247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xll_22247/10_2026/6xll_22247.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xll_22247/10_2026/6xll_22247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xll_22247/10_2026/6xll_22247.map" } resolution = 2.7 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= 0.157 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 103 5.49 5 Mg 1 5.21 5 S 129 5.16 5 C 19191 2.51 5 N 5516 2.21 5 O 6192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31134 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: 3878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3878 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 461} Chain breaks: 2 Chain: "N" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "T" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 979 Classifications: {'DNA': 48} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "R" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'GTP': 1} Classifications: {'RNAv2': 4, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3, None: 1} Not linked: pdbres="GTP R 1 " pdbres=" C R 2 " 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 47.871 44.912 102.226 1.00 99.55 S ATOM 14527 SG CYS D 72 49.530 43.233 104.731 1.00103.46 S ATOM 14635 SG CYS D 85 46.279 44.246 105.601 1.00103.36 S ATOM 14659 SG CYS D 88 49.742 46.469 105.764 1.00101.49 S ATOM 20347 SG CYS D 814 34.065 108.338 86.644 1.00 84.51 S ATOM 20912 SG CYS D 888 37.011 106.549 86.954 1.00 81.65 S ATOM 20963 SG CYS D 895 35.589 106.670 84.135 1.00 76.46 S ATOM 20984 SG CYS D 898 37.204 109.440 84.941 1.00 78.50 S Time building chain proxies: 6.13, per 1000 atoms: 0.20 Number of scatterers: 31134 At special positions: 0 Unit cell: (150.629, 173.29, 182.621, 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 129 16.00 P 103 15.00 Mg 1 11.99 O 6192 8.00 N 5516 7.00 C 19191 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 993.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " 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 88 " pdb=" ZN D1503 " 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 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 12 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 49 sheets defined 43.0% alpha, 15.7% beta 43 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.625A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 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 158 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: 3.763A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.521A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.634A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.725A 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: 3.685A pdb=" N ARG C 245 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.751A pdb=" N ILE C 292 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 345 through 352 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.862A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 removed outlier: 3.506A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.734A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.597A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 removed outlier: 3.597A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.929A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.598A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.591A 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 687 removed outlier: 4.262A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (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: 4.438A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 985 through 990 removed outlier: 3.825A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 997 Processing helix chain 'C' and resid 1006 through 1037 removed outlier: 4.105A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C1031 " --> pdb=" O LYS C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.608A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.586A pdb=" N THR C1115 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C1130 " --> pdb=" O ASP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.851A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1331 Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.529A pdb=" N SER D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.515A pdb=" N HIS D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 77 through 81' Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.589A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.500A 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 139 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.933A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.867A 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: 4.046A 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: 3.960A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (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 503 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.851A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 634 removed outlier: 3.743A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.865A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.053A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 4.082A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.507A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.539A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 removed outlier: 3.597A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.801A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.623A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1294 Processing helix chain 'D' and resid 1308 through 1314 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.567A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1347 through 1353 removed outlier: 3.603A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.669A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.875A pdb=" N THR F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 136 removed outlier: 3.709A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.816A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 removed outlier: 4.622A pdb=" N ALA F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 257 Processing helix chain 'F' and resid 262 through 292 removed outlier: 3.722A pdb=" N PHE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N CYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL F 292 " --> pdb=" O MET F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 307 removed outlier: 4.261A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE F 306 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 removed outlier: 3.514A pdb=" N ASN F 317 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 323 removed outlier: 3.713A pdb=" N MET F 322 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 330 Processing helix chain 'F' and resid 331 through 334 Processing helix chain 'F' and resid 337 through 351 removed outlier: 3.782A pdb=" N GLN F 342 " --> pdb=" O HIS F 338 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN F 345 " --> pdb=" O LEU F 341 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 383 removed outlier: 3.520A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 removed outlier: 3.656A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 400 through 418 Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.929A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 447 removed outlier: 3.879A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA F 447 " --> pdb=" O ILE F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 Processing helix chain 'F' and resid 479 through 487 removed outlier: 4.572A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 510 through 514 removed outlier: 4.153A pdb=" N ASP F 513 " --> pdb=" O PRO F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 550 Processing helix chain 'F' and resid 552 through 563 Processing helix chain 'F' and resid 572 through 581 Processing helix chain 'F' and resid 583 through 599 removed outlier: 3.594A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 removed outlier: 4.009A pdb=" N SER F 609 " --> pdb=" O GLU F 605 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 20 removed outlier: 5.139A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N HIS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.760A 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: 7.341A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (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 removed outlier: 6.563A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) 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 14 removed outlier: 6.457A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.209A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 196 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG B 191 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 105 removed outlier: 7.634A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.908A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.488A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.481A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 160 removed outlier: 4.811A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 240 Processing sheet with id=AC1, first strand: chain 'C' and resid 250 through 251 Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 303 removed outlier: 6.901A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.517A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.529A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.658A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 6.964A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.125A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.670A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD5, first strand: chain 'C' and resid 1268 through 1270 Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1337 Processing sheet with id=AD7, first strand: chain 'D' and resid 103 through 112 removed outlier: 9.789A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 159 through 160 removed outlier: 6.773A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 253 through 254 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 820 through 822 Processing sheet with id=AE5, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.520A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP D 830 " --> pdb=" O GLU D 827 " (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: 3.911A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 957 through 961 removed outlier: 4.443A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 6.163A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1099 through 1100 removed outlier: 3.614A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE D1115 " --> pdb=" O GLY D1033 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1046 through 1049 Processing sheet with id=AF3, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AF4, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 4.590A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 1266 hydrogen bonds defined for protein. 3540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 228 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 7.99 Time building geometry restraints manager: 3.52 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: 9034 1.33 - 1.45: 5308 1.45 - 1.57: 17040 1.57 - 1.69: 202 1.69 - 1.81: 227 Bond restraints: 31811 Sorted by residual: bond pdb=" C3' DT T 14 " pdb=" O3' DT T 14 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.31e+01 bond pdb=" C1' DC N 78 " pdb=" N1 DC N 78 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" C3' DT T 48 " pdb=" C2' DT T 48 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA N 41 " pdb=" C2' DA N 41 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.31e+00 bond pdb=" C1' DC T 13 " pdb=" N1 DC T 13 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.69e+00 ... (remaining 31806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 41844 2.01 - 4.01: 1396 4.01 - 6.02: 129 6.02 - 8.02: 26 8.02 - 10.03: 6 Bond angle restraints: 43401 Sorted by residual: angle pdb=" N VAL C 615 " pdb=" CA VAL C 615 " pdb=" C VAL C 615 " ideal model delta sigma weight residual 108.17 99.78 8.39 1.40e+00 5.10e-01 3.59e+01 angle pdb=" N3 DT N 38 " pdb=" C4 DT N 38 " pdb=" O4 DT N 38 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT N 61 " pdb=" C4 DT N 61 " pdb=" O4 DT N 61 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.94e+01 angle pdb=" O4 DT N 38 " pdb=" C4 DT N 38 " pdb=" C5 DT N 38 " ideal model delta sigma weight residual 124.90 121.82 3.08 7.00e-01 2.04e+00 1.94e+01 angle pdb=" N3 DT T 8 " pdb=" C4 DT T 8 " pdb=" O4 DT T 8 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 43396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.72: 17946 27.72 - 55.45: 1188 55.45 - 83.17: 123 83.17 - 110.89: 11 110.89 - 138.61: 2 Dihedral angle restraints: 19270 sinusoidal: 8666 harmonic: 10604 Sorted by residual: dihedral pdb=" CA PHE C1265 " pdb=" C PHE C1265 " pdb=" N GLY C1266 " pdb=" CA GLY C1266 " ideal model delta harmonic sigma weight residual 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual 180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" O3A GTP R 1 " pdb=" O3B GTP R 1 " pdb=" PB GTP R 1 " pdb=" PG GTP R 1 " ideal model delta sinusoidal sigma weight residual -56.21 -164.38 108.18 1 2.00e+01 2.50e-03 3.15e+01 ... (remaining 19267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4048 0.070 - 0.141: 845 0.141 - 0.211: 58 0.211 - 0.282: 4 0.282 - 0.352: 3 Chirality restraints: 4958 Sorted by residual: chirality pdb=" CA VAL C 615 " pdb=" N VAL C 615 " pdb=" C VAL C 615 " pdb=" CB VAL C 615 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA ARG C 540 " pdb=" N ARG C 540 " pdb=" C ARG C 540 " pdb=" CB ARG C 540 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+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 -2.48 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 4955 not shown) Planarity restraints: 5300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 212 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO B 213 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 75 " 0.027 2.00e-02 2.50e+03 1.58e-02 4.98e+00 pdb=" CG TYR D 75 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR D 75 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 75 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 75 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 75 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR D 75 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 75 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C1257 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO C1258 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C1258 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C1258 " -0.030 5.00e-02 4.00e+02 ... (remaining 5297 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 130 2.45 - 3.06: 19447 3.06 - 3.68: 47817 3.68 - 4.29: 73455 4.29 - 4.90: 121514 Nonbonded interactions: 262363 Sorted by model distance: nonbonded pdb=" O3' U R 5 " pdb="MG MG D1501 " model vdw 1.839 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.019 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 2.068 2.170 nonbonded pdb=" O LEU D 510 " pdb=" OG1 THR D 514 " model vdw 2.212 3.040 ... (remaining 262358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 159 or resid 169 through 234)) selection = (chain 'B' and resid 5 through 234) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 34.310 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.010 0.572 31820 Z= 0.440 Angle : 0.858 27.595 43413 Z= 0.502 Chirality : 0.055 0.352 4958 Planarity : 0.006 0.061 5300 Dihedral : 17.140 138.613 12434 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.06 % Allowed : 5.87 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -3.11 (0.11), residues: 3661 helix: -2.16 (0.11), residues: 1446 sheet: -1.91 (0.24), residues: 373 loop : -1.95 (0.12), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1246 TYR 0.027 0.003 TYR D 75 PHE 0.017 0.002 PHE D 338 TRP 0.009 0.002 TRP D 33 HIS 0.009 0.002 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00898 / 0.41 (31811) covalent geometry : angle 0.83535 / 0.50 (43401) hydrogen bonds : bond 0.14698 / 9.91 ( 1376) hydrogen bonds : angle 6.77217 / 4.71 ( 3768) metal coordination : bond 0.27535 / 14.04 ( 8) metal coordination : angle 11.79728 / 7.12 ( 12) Misc. bond : bond 0.04192 / 2.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 402 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7870 (ttmm) REVERT: A 103 ASN cc_start: 0.8703 (m-40) cc_final: 0.8413 (m-40) REVERT: A 125 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8028 (tttt) REVERT: A 181 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7391 (mt-10) REVERT: A 205 MET cc_start: 0.8677 (ttt) cc_final: 0.8244 (ttp) REVERT: B 7 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7476 (pp20) REVERT: B 10 LYS cc_start: 0.9121 (mttp) cc_final: 0.8838 (mttp) REVERT: B 145 LYS cc_start: 0.8326 (tttt) cc_final: 0.7955 (ttmm) REVERT: B 152 TYR cc_start: 0.8791 (t80) cc_final: 0.8541 (t80) REVERT: B 156 SER cc_start: 0.8696 (m) cc_final: 0.8362 (p) REVERT: B 170 ARG cc_start: 0.6846 (mtm-85) cc_final: 0.6072 (mpp-170) REVERT: C 46 GLN cc_start: 0.8537 (mt0) cc_final: 0.8304 (mt0) REVERT: C 74 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7561 (ttp-110) REVERT: C 119 GLU cc_start: 0.8490 (pp20) cc_final: 0.8013 (pp20) REVERT: C 200 ARG cc_start: 0.8346 (mmm160) cc_final: 0.7850 (mmm-85) REVERT: C 229 ILE cc_start: 0.8104 (mt) cc_final: 0.7849 (mp) REVERT: C 299 LYS cc_start: 0.7466 (tttp) cc_final: 0.7141 (mtpt) REVERT: C 314 ASN cc_start: 0.8681 (t0) cc_final: 0.8339 (t0) REVERT: C 343 HIS cc_start: 0.6896 (m90) cc_final: 0.6440 (m90) REVERT: C 377 THR cc_start: 0.8038 (p) cc_final: 0.7794 (t) REVERT: C 407 ARG cc_start: 0.7482 (tpp80) cc_final: 0.7081 (ttp-170) REVERT: C 470 ARG cc_start: 0.7447 (mtt-85) cc_final: 0.7144 (mtm-85) REVERT: C 479 LEU cc_start: 0.7700 (mt) cc_final: 0.7353 (mt) REVERT: C 492 MET cc_start: 0.8366 (mtp) cc_final: 0.7942 (mtp) REVERT: C 503 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7819 (mtpm) REVERT: C 515 MET cc_start: 0.8593 (ttp) cc_final: 0.8081 (ttm) REVERT: C 704 MET cc_start: 0.8315 (mmm) cc_final: 0.8115 (mtp) REVERT: C 719 LYS cc_start: 0.8470 (mtmm) cc_final: 0.7513 (mmtt) REVERT: C 805 MET cc_start: 0.8814 (ptm) cc_final: 0.8260 (ptm) REVERT: C 954 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7971 (mttp) REVERT: C 958 LYS cc_start: 0.7326 (tttt) cc_final: 0.7002 (tttp) REVERT: C 1131 MET cc_start: 0.8288 (mtt) cc_final: 0.7903 (mtt) REVERT: C 1180 MET cc_start: 0.8695 (ttp) cc_final: 0.8466 (ttp) REVERT: C 1315 MET cc_start: 0.8610 (ptm) cc_final: 0.8132 (ptp) REVERT: D 130 MET cc_start: 0.8563 (ttt) cc_final: 0.8356 (ttt) REVERT: D 147 ILE cc_start: 0.8155 (pt) cc_final: 0.7851 (mt) REVERT: D 200 GLN cc_start: 0.7439 (tt0) cc_final: 0.7041 (tm-30) REVERT: D 213 LYS cc_start: 0.8150 (tttt) cc_final: 0.7918 (tttt) REVERT: D 221 ILE cc_start: 0.8143 (mt) cc_final: 0.7930 (mt) REVERT: D 322 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7882 (mtp-110) REVERT: D 372 MET cc_start: 0.8779 (mtp) cc_final: 0.8117 (mtm) REVERT: D 375 GLU cc_start: 0.8275 (tp30) cc_final: 0.7968 (mm-30) REVERT: D 386 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6998 (mt-10) REVERT: D 525 MET cc_start: 0.8893 (ptp) cc_final: 0.8182 (ptm) REVERT: D 649 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7306 (mmtt) REVERT: D 712 GLN cc_start: 0.7320 (mt0) cc_final: 0.6912 (mm-40) REVERT: D 715 LYS cc_start: 0.8907 (ptmt) cc_final: 0.8665 (mtpt) REVERT: D 724 MET cc_start: 0.8137 (mtm) cc_final: 0.7703 (mtm) REVERT: D 743 MET cc_start: 0.8599 (ptp) cc_final: 0.8105 (ptp) REVERT: D 774 ILE cc_start: 0.8328 (mt) cc_final: 0.8106 (mp) REVERT: D 1095 MET cc_start: 0.5740 (ptp) cc_final: 0.5461 (ptt) REVERT: D 1149 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.6814 (mtp-110) REVERT: D 1172 LYS cc_start: 0.7121 (mttm) cc_final: 0.6830 (ptpp) REVERT: D 1174 ARG cc_start: 0.7196 (ttm170) cc_final: 0.6446 (tmt90) REVERT: D 1188 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6828 (mm-30) REVERT: D 1189 MET cc_start: 0.8028 (mmm) cc_final: 0.7789 (mmp) REVERT: D 1193 TRP cc_start: 0.7614 (p-90) cc_final: 0.7271 (p90) REVERT: D 1205 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7684 (mp0) REVERT: D 1260 MET cc_start: 0.8948 (mtp) cc_final: 0.8736 (mtm) REVERT: D 1276 GLU cc_start: 0.7910 (mp0) cc_final: 0.7561 (mp0) REVERT: D 1372 ARG cc_start: 0.7291 (mmt180) cc_final: 0.5844 (tmm-80) REVERT: E 67 ARG cc_start: 0.7260 (tpt170) cc_final: 0.6814 (mtp-110) REVERT: E 70 GLN cc_start: 0.7158 (tt0) cc_final: 0.6744 (tm-30) REVERT: F 322 MET cc_start: 0.3810 (tpt) cc_final: 0.2712 (ppp) REVERT: F 456 MET cc_start: 0.7780 (tpp) cc_final: 0.7013 (tpt) REVERT: F 567 MET cc_start: 0.8175 (mtt) cc_final: 0.7847 (mtm) REVERT: F 581 ASP cc_start: 0.6961 (m-30) cc_final: 0.6363 (p0) outliers start: 2 outliers final: 3 residues processed: 404 average time/residue: 0.8330 time to fit residues: 384.8002 Evaluate side-chains 288 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 285 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 HIS B 66 HIS B 103 ASN C 31 GLN C 46 GLN C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 276 GLN C 518 ASN C 582 ASN C 620 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS C1257 GLN D 94 GLN D 274 ASN D 364 HIS D 424 ASN D 777 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D 910 ASN D1084 GLN D1126 GLN D1366 HIS E 62 GLN F 227 GLN F 258 GLN F 331 HIS F 357 GLN F 383 ASN F 446 GLN F 472 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.164310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101795 restraints weight = 39258.522| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.21 r_work: 0.3153 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31820 Z= 0.145 Angle : 0.608 9.187 43413 Z= 0.326 Chirality : 0.044 0.211 4958 Planarity : 0.005 0.054 5300 Dihedral : 16.165 140.472 5148 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.59 % Allowed : 12.05 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -1.71 (0.13), residues: 3661 helix: -0.54 (0.13), residues: 1444 sheet: -1.74 (0.25), residues: 376 loop : -1.42 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D1173 TYR 0.032 0.001 TYR F 137 PHE 0.018 0.001 PHE C 337 TRP 0.011 0.001 TRP D1193 HIS 0.011 0.001 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (31811) covalent geometry : angle 0.60682 / 0.33 (43401) hydrogen bonds : bond 0.04323 / 2.90 ( 1376) hydrogen bonds : angle 5.09099 / 3.54 ( 3768) metal coordination : bond 0.00859 / 0.41 ( 8) metal coordination : angle 2.75697 / 1.50 ( 12) Misc. bond : bond 0.00322 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 315 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8364 (mm) REVERT: A 86 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7717 (ttmm) REVERT: A 95 LYS cc_start: 0.8363 (mttp) cc_final: 0.8129 (mttp) REVERT: A 103 ASN cc_start: 0.8529 (m-40) cc_final: 0.8288 (m-40) REVERT: A 125 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7634 (tttt) REVERT: A 145 LYS cc_start: 0.8399 (ttpt) cc_final: 0.8109 (ttpp) REVERT: A 181 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7288 (mt-10) REVERT: B 7 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7338 (pp20) REVERT: B 10 LYS cc_start: 0.8431 (mttp) cc_final: 0.8108 (mttm) REVERT: B 51 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8200 (mmm) REVERT: B 145 LYS cc_start: 0.7994 (tttt) cc_final: 0.7660 (ttmm) REVERT: B 152 TYR cc_start: 0.8784 (t80) cc_final: 0.8476 (t80) REVERT: B 156 SER cc_start: 0.8436 (m) cc_final: 0.8043 (p) REVERT: B 170 ARG cc_start: 0.6967 (mtm-85) cc_final: 0.5818 (mpp-170) REVERT: C 74 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7393 (ptm-80) REVERT: C 119 GLU cc_start: 0.8460 (pp20) cc_final: 0.7921 (pp20) REVERT: C 200 ARG cc_start: 0.8319 (mmm160) cc_final: 0.7669 (mmm-85) REVERT: C 299 LYS cc_start: 0.7063 (tttp) cc_final: 0.6839 (mtpt) REVERT: C 314 ASN cc_start: 0.8167 (t0) cc_final: 0.7940 (t0) REVERT: C 357 ASN cc_start: 0.8030 (p0) cc_final: 0.7795 (p0) REVERT: C 377 THR cc_start: 0.7695 (p) cc_final: 0.7467 (t) REVERT: C 394 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7473 (mtm-85) REVERT: C 407 ARG cc_start: 0.7794 (tpp80) cc_final: 0.7082 (ttp-170) REVERT: C 470 ARG cc_start: 0.7274 (mtt-85) cc_final: 0.6819 (mtm-85) REVERT: C 479 LEU cc_start: 0.6826 (mt) cc_final: 0.6509 (mt) REVERT: C 492 MET cc_start: 0.8187 (mtp) cc_final: 0.7842 (mtp) REVERT: C 503 LYS cc_start: 0.7837 (ttmt) cc_final: 0.7562 (mtpm) REVERT: C 515 MET cc_start: 0.8846 (ttp) cc_final: 0.8414 (ttm) REVERT: C 582 ASN cc_start: 0.7975 (t0) cc_final: 0.7744 (t160) REVERT: C 641 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7466 (pp20) REVERT: C 704 MET cc_start: 0.8308 (mmm) cc_final: 0.8074 (mtp) REVERT: C 719 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7109 (mmtt) REVERT: C 805 MET cc_start: 0.8983 (ptm) cc_final: 0.8486 (ptm) REVERT: C 814 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7680 (t0) REVERT: C 954 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7718 (mttp) REVERT: C 958 LYS cc_start: 0.6784 (tttt) cc_final: 0.6554 (tttp) REVERT: C 1131 MET cc_start: 0.7899 (mtt) cc_final: 0.7595 (mtt) REVERT: C 1315 MET cc_start: 0.8652 (ptm) cc_final: 0.8092 (ptp) REVERT: D 151 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8073 (mmm) REVERT: D 200 GLN cc_start: 0.7118 (tt0) cc_final: 0.6773 (tm-30) REVERT: D 217 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7733 (mp) REVERT: D 322 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7743 (mtp-110) REVERT: D 372 MET cc_start: 0.8720 (mtp) cc_final: 0.8490 (ttp) REVERT: D 375 GLU cc_start: 0.8470 (tp30) cc_final: 0.8068 (mm-30) REVERT: D 386 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6998 (mt-10) REVERT: D 443 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8304 (mt-10) REVERT: D 525 MET cc_start: 0.8591 (ptp) cc_final: 0.8012 (ptm) REVERT: D 649 LYS cc_start: 0.6939 (mmmt) cc_final: 0.6601 (mmtt) REVERT: D 704 GLU cc_start: 0.5381 (OUTLIER) cc_final: 0.4576 (tm-30) REVERT: D 712 GLN cc_start: 0.6634 (mt0) cc_final: 0.6233 (mm-40) REVERT: D 715 LYS cc_start: 0.8934 (ptmt) cc_final: 0.8393 (mtpp) REVERT: D 724 MET cc_start: 0.8000 (mtm) cc_final: 0.7594 (mtm) REVERT: D 743 MET cc_start: 0.8706 (ptp) cc_final: 0.8286 (ptp) REVERT: D 1095 MET cc_start: 0.5816 (ptp) cc_final: 0.5561 (ptp) REVERT: D 1149 ARG cc_start: 0.7176 (ttm-80) cc_final: 0.6568 (mtp-110) REVERT: D 1152 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7200 (pm20) REVERT: D 1174 ARG cc_start: 0.6968 (ttm170) cc_final: 0.6243 (tmt90) REVERT: D 1188 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7090 (mm-30) REVERT: D 1189 MET cc_start: 0.7996 (mmm) cc_final: 0.7564 (mmp) REVERT: D 1193 TRP cc_start: 0.7809 (p-90) cc_final: 0.7436 (p90) REVERT: D 1205 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7716 (mp0) REVERT: D 1260 MET cc_start: 0.8856 (mtp) cc_final: 0.8635 (mtm) REVERT: D 1276 GLU cc_start: 0.7882 (mp0) cc_final: 0.7326 (mp0) REVERT: D 1372 ARG cc_start: 0.6563 (mmt180) cc_final: 0.5289 (tmm-80) REVERT: E 67 ARG cc_start: 0.6992 (tpt170) cc_final: 0.6324 (mtp-110) REVERT: E 70 GLN cc_start: 0.6923 (tt0) cc_final: 0.6364 (tm-30) REVERT: F 561 MET cc_start: 0.6655 (tpp) cc_final: 0.6416 (tmm) REVERT: F 567 MET cc_start: 0.8352 (mtt) cc_final: 0.7986 (mtm) REVERT: F 578 LYS cc_start: 0.7682 (mttt) cc_final: 0.7410 (mptt) outliers start: 50 outliers final: 12 residues processed: 348 average time/residue: 0.7850 time to fit residues: 315.7960 Evaluate side-chains 299 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 1152 GLU Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 551 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [258, 311, 332, 226, 319, 44, 268, 118, 8, 143, 152] chunk 258 optimal weight: 0.7980 chunk 311 optimal weight: 0.4980 chunk 332 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 319 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.163595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.100895 restraints weight = 39482.744| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.21 r_work: 0.3138 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31820 Z= 0.171 Angle : 0.590 11.175 43413 Z= 0.313 Chirality : 0.044 0.231 4958 Planarity : 0.004 0.053 5300 Dihedral : 16.050 140.347 5146 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.12 % Allowed : 13.80 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -1.17 (0.13), residues: 3661 helix: 0.00 (0.13), residues: 1460 sheet: -1.46 (0.25), residues: 383 loop : -1.22 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 368 TYR 0.025 0.001 TYR F 137 PHE 0.014 0.001 PHE C 405 TRP 0.006 0.001 TRP F 434 HIS 0.005 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (31811) covalent geometry : angle 0.58861 / 0.31 (43401) hydrogen bonds : bond 0.04103 / 2.75 ( 1376) hydrogen bonds : angle 4.77367 / 3.31 ( 3768) metal coordination : bond 0.00884 / 0.43 ( 8) metal coordination : angle 2.55750 / 1.41 ( 12) Misc. bond : bond 0.00108 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 303 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8276 (mm) REVERT: A 86 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7711 (ttmm) REVERT: A 95 LYS cc_start: 0.8588 (mttp) cc_final: 0.8288 (mttp) REVERT: A 97 GLU cc_start: 0.8687 (tt0) cc_final: 0.7947 (tt0) REVERT: A 103 ASN cc_start: 0.8543 (m-40) cc_final: 0.8286 (m-40) REVERT: A 125 LYS cc_start: 0.8066 (ttpt) cc_final: 0.7633 (tttt) REVERT: A 181 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7268 (mt-10) REVERT: B 7 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7345 (pp20) REVERT: B 10 LYS cc_start: 0.8804 (mttp) cc_final: 0.8497 (mttp) REVERT: B 145 LYS cc_start: 0.7986 (tttt) cc_final: 0.7646 (ttmm) REVERT: B 152 TYR cc_start: 0.8804 (t80) cc_final: 0.8490 (t80) REVERT: B 156 SER cc_start: 0.8336 (m) cc_final: 0.7948 (p) REVERT: B 170 ARG cc_start: 0.7051 (mtm-85) cc_final: 0.5847 (mpp-170) REVERT: C 74 ARG cc_start: 0.7853 (ttp-110) cc_final: 0.7500 (ptm-80) REVERT: C 119 GLU cc_start: 0.8455 (pp20) cc_final: 0.7898 (pp20) REVERT: C 200 ARG cc_start: 0.8338 (mmm160) cc_final: 0.7664 (mmm-85) REVERT: C 299 LYS cc_start: 0.7046 (tttp) cc_final: 0.6773 (mtpt) REVERT: C 314 ASN cc_start: 0.8151 (t0) cc_final: 0.7948 (t0) REVERT: C 343 HIS cc_start: 0.6732 (m90) cc_final: 0.6490 (m-70) REVERT: C 357 ASN cc_start: 0.7951 (p0) cc_final: 0.7739 (p0) REVERT: C 369 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7227 (tmt) REVERT: C 377 THR cc_start: 0.7639 (p) cc_final: 0.7413 (t) REVERT: C 407 ARG cc_start: 0.7816 (tpp80) cc_final: 0.7251 (mtp180) REVERT: C 470 ARG cc_start: 0.7263 (mtt-85) cc_final: 0.6840 (mtm-85) REVERT: C 479 LEU cc_start: 0.6768 (mt) cc_final: 0.6473 (mt) REVERT: C 492 MET cc_start: 0.8207 (mtp) cc_final: 0.7889 (mtp) REVERT: C 503 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7666 (mtpm) REVERT: C 515 MET cc_start: 0.8846 (ttp) cc_final: 0.8440 (ttm) REVERT: C 529 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6946 (tpm170) REVERT: C 582 ASN cc_start: 0.7880 (t0) cc_final: 0.7674 (t160) REVERT: C 641 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7449 (pp20) REVERT: C 719 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7132 (mmtt) REVERT: C 814 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7717 (t0) REVERT: C 954 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7681 (mttp) REVERT: C 958 LYS cc_start: 0.6735 (tttt) cc_final: 0.6494 (tttp) REVERT: D 60 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8235 (ttp-170) REVERT: D 151 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8041 (mmm) REVERT: D 200 GLN cc_start: 0.6945 (tt0) cc_final: 0.6598 (tm-30) REVERT: D 217 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7718 (mp) REVERT: D 322 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.7915 (mtp-110) REVERT: D 372 MET cc_start: 0.8702 (mtp) cc_final: 0.8401 (ttp) REVERT: D 375 GLU cc_start: 0.8461 (tp30) cc_final: 0.8053 (mm-30) REVERT: D 386 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7155 (mt-10) REVERT: D 443 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8319 (mt-10) REVERT: D 525 MET cc_start: 0.8599 (ptp) cc_final: 0.8067 (ptm) REVERT: D 649 LYS cc_start: 0.6974 (mmmt) cc_final: 0.6624 (mmtt) REVERT: D 704 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.4631 (tm-30) REVERT: D 712 GLN cc_start: 0.6616 (mt0) cc_final: 0.6239 (mm-40) REVERT: D 715 LYS cc_start: 0.8925 (ptmt) cc_final: 0.8400 (mtpt) REVERT: D 724 MET cc_start: 0.7956 (mtm) cc_final: 0.7568 (mtm) REVERT: D 743 MET cc_start: 0.8624 (ptp) cc_final: 0.8235 (ptp) REVERT: D 792 ASN cc_start: 0.7590 (t0) cc_final: 0.7243 (m110) REVERT: D 802 ASP cc_start: 0.7734 (m-30) cc_final: 0.7122 (m-30) REVERT: D 827 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7563 (mt-10) REVERT: D 1149 ARG cc_start: 0.7159 (ttm-80) cc_final: 0.6560 (mtp-110) REVERT: D 1174 ARG cc_start: 0.6908 (ttm170) cc_final: 0.6215 (tmt90) REVERT: D 1188 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6864 (mm-30) REVERT: D 1189 MET cc_start: 0.7849 (mmm) cc_final: 0.7532 (mmp) REVERT: D 1193 TRP cc_start: 0.7794 (p-90) cc_final: 0.7482 (p90) REVERT: D 1205 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7709 (mp0) REVERT: D 1260 MET cc_start: 0.8878 (mtp) cc_final: 0.8638 (mtm) REVERT: D 1276 GLU cc_start: 0.7886 (mp0) cc_final: 0.7347 (mp0) REVERT: D 1372 ARG cc_start: 0.6511 (mmt180) cc_final: 0.5225 (tmm-80) REVERT: E 35 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.6851 (mtmm) REVERT: E 67 ARG cc_start: 0.7022 (tpt170) cc_final: 0.6342 (mtp-110) REVERT: E 70 GLN cc_start: 0.6930 (tt0) cc_final: 0.6366 (tm-30) REVERT: F 567 MET cc_start: 0.8547 (mtt) cc_final: 0.8136 (mtm) REVERT: F 578 LYS cc_start: 0.7656 (mttt) cc_final: 0.7358 (mptt) outliers start: 67 outliers final: 19 residues processed: 349 average time/residue: 0.7691 time to fit residues: 311.4445 Evaluate side-chains 304 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 276 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 527 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [7, 343, 217, 120, 26, 303, 357, 143, 92, 275, 142] chunk 7 optimal weight: 0.6980 chunk 343 optimal weight: 0.0870 chunk 217 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 303 optimal weight: 0.0870 chunk 357 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 275 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN C 41 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.164225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.101636 restraints weight = 39260.836| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.20 r_work: 0.3168 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31820 Z= 0.149 Angle : 0.565 8.851 43413 Z= 0.300 Chirality : 0.043 0.237 4958 Planarity : 0.004 0.051 5300 Dihedral : 15.981 140.436 5143 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.47 % Allowed : 15.03 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -0.85 (0.14), residues: 3661 helix: 0.33 (0.14), residues: 1472 sheet: -1.42 (0.25), residues: 388 loop : -1.07 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1173 TYR 0.021 0.001 TYR F 137 PHE 0.014 0.001 PHE C 405 TRP 0.011 0.001 TRP F 326 HIS 0.004 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (31811) covalent geometry : angle 0.56370 / 0.30 (43401) hydrogen bonds : bond 0.03794 / 2.54 ( 1376) hydrogen bonds : angle 4.58121 / 3.17 ( 3768) metal coordination : bond 0.00592 / 0.29 ( 8) metal coordination : angle 2.22286 / 1.22 ( 12) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 293 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6851 (ttm110) REVERT: A 16 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 86 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7720 (ttmm) REVERT: A 95 LYS cc_start: 0.8621 (mttp) cc_final: 0.8297 (mttp) REVERT: A 103 ASN cc_start: 0.8490 (m-40) cc_final: 0.8262 (m-40) REVERT: A 120 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7451 (p0) REVERT: A 125 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7691 (tttt) REVERT: A 145 LYS cc_start: 0.8386 (ttpt) cc_final: 0.8095 (ttpp) REVERT: A 181 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7317 (mt-10) REVERT: B 7 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7056 (pp20) REVERT: B 10 LYS cc_start: 0.8821 (mttp) cc_final: 0.8517 (mttm) REVERT: B 18 GLN cc_start: 0.7649 (mp10) cc_final: 0.7298 (mm110) REVERT: B 78 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7707 (mp) REVERT: B 145 LYS cc_start: 0.8054 (tttt) cc_final: 0.7729 (ttmm) REVERT: B 152 TYR cc_start: 0.8807 (t80) cc_final: 0.8582 (t80) REVERT: B 170 ARG cc_start: 0.6980 (mtm-85) cc_final: 0.5686 (mpp-170) REVERT: C 74 ARG cc_start: 0.7902 (ttp-110) cc_final: 0.7618 (ptm-80) REVERT: C 119 GLU cc_start: 0.8511 (pp20) cc_final: 0.7950 (pp20) REVERT: C 200 ARG cc_start: 0.8366 (mmm160) cc_final: 0.7650 (mmm-85) REVERT: C 299 LYS cc_start: 0.7139 (tttp) cc_final: 0.6854 (mtpt) REVERT: C 369 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7379 (tmt) REVERT: C 377 THR cc_start: 0.7657 (p) cc_final: 0.7434 (t) REVERT: C 407 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7279 (mtp180) REVERT: C 446 ASP cc_start: 0.8330 (p0) cc_final: 0.7982 (m-30) REVERT: C 470 ARG cc_start: 0.7294 (mtt-85) cc_final: 0.6906 (mtm-85) REVERT: C 479 LEU cc_start: 0.6793 (mt) cc_final: 0.6497 (mt) REVERT: C 492 MET cc_start: 0.8289 (mtp) cc_final: 0.7959 (mtp) REVERT: C 503 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7734 (mtpm) REVERT: C 515 MET cc_start: 0.8875 (ttp) cc_final: 0.8481 (ttm) REVERT: C 529 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7078 (tpm170) REVERT: C 582 ASN cc_start: 0.7895 (t0) cc_final: 0.7659 (t160) REVERT: C 641 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7447 (pp20) REVERT: C 719 LYS cc_start: 0.8259 (mtmm) cc_final: 0.7231 (mmtt) REVERT: C 814 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7731 (t0) REVERT: C 954 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7732 (mttp) REVERT: C 958 LYS cc_start: 0.6806 (tttt) cc_final: 0.6556 (tttp) REVERT: D 60 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8280 (ttp-170) REVERT: D 151 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7981 (mmm) REVERT: D 200 GLN cc_start: 0.7134 (tt0) cc_final: 0.6779 (tm-30) REVERT: D 217 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7721 (mp) REVERT: D 322 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.7948 (ttp80) REVERT: D 372 MET cc_start: 0.8747 (mtp) cc_final: 0.8428 (ttp) REVERT: D 375 GLU cc_start: 0.8508 (tp30) cc_final: 0.8122 (mm-30) REVERT: D 386 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7162 (mt-10) REVERT: D 443 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8336 (mt-10) REVERT: D 525 MET cc_start: 0.8574 (ptp) cc_final: 0.8011 (ptm) REVERT: D 649 LYS cc_start: 0.7006 (mmmt) cc_final: 0.6635 (mmtt) REVERT: D 704 GLU cc_start: 0.5405 (OUTLIER) cc_final: 0.4646 (tm-30) REVERT: D 712 GLN cc_start: 0.6654 (mt0) cc_final: 0.6247 (mm-40) REVERT: D 715 LYS cc_start: 0.8938 (ptmt) cc_final: 0.8418 (mtpt) REVERT: D 724 MET cc_start: 0.8184 (mtm) cc_final: 0.7789 (mtm) REVERT: D 743 MET cc_start: 0.8588 (ptp) cc_final: 0.8238 (ptp) REVERT: D 792 ASN cc_start: 0.7616 (t0) cc_final: 0.7302 (m110) REVERT: D 827 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7578 (mt-10) REVERT: D 1149 ARG cc_start: 0.7176 (ttm-80) cc_final: 0.6593 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7178 (ttm170) cc_final: 0.6382 (tmt90) REVERT: D 1188 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6993 (mm-30) REVERT: D 1192 LYS cc_start: 0.6429 (mppt) cc_final: 0.5762 (mppt) REVERT: D 1193 TRP cc_start: 0.7854 (p-90) cc_final: 0.7621 (p90) REVERT: D 1205 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7724 (mp0) REVERT: D 1260 MET cc_start: 0.8906 (mtp) cc_final: 0.8652 (mtm) REVERT: D 1372 ARG cc_start: 0.6500 (mmt180) cc_final: 0.5215 (tmm-80) REVERT: E 67 ARG cc_start: 0.7001 (tpt170) cc_final: 0.6297 (mtp-110) REVERT: E 70 GLN cc_start: 0.7063 (tt0) cc_final: 0.6482 (tm-30) REVERT: F 485 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: F 567 MET cc_start: 0.8618 (mtt) cc_final: 0.8175 (mtm) REVERT: F 578 LYS cc_start: 0.7609 (mttt) cc_final: 0.7310 (mptt) outliers start: 78 outliers final: 28 residues processed: 345 average time/residue: 0.7762 time to fit residues: 311.1788 Evaluate side-chains 320 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 527 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [19, 196, 26, 153, 49, 338, 132, 292, 236, 173, 164] chunk 19 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 338 optimal weight: 20.0000 chunk 132 optimal weight: 0.5980 chunk 292 optimal weight: 9.9990 chunk 236 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 GLN E 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.165121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102682 restraints weight = 39328.503| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.21 r_work: 0.3182 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31820 Z= 0.125 Angle : 0.542 9.133 43413 Z= 0.289 Chirality : 0.042 0.239 4958 Planarity : 0.004 0.051 5300 Dihedral : 15.913 140.344 5143 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.66 % Allowed : 15.70 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -0.58 (0.14), residues: 3661 helix: 0.59 (0.14), residues: 1472 sheet: -1.37 (0.26), residues: 371 loop : -0.94 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 214 TYR 0.018 0.001 TYR F 137 PHE 0.025 0.001 PHE C 337 TRP 0.008 0.001 TRP D1193 HIS 0.004 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (31811) covalent geometry : angle 0.54095 / 0.29 (43401) hydrogen bonds : bond 0.03615 / 2.41 ( 1376) hydrogen bonds : angle 4.44181 / 3.07 ( 3768) metal coordination : bond 0.00461 / 0.22 ( 8) metal coordination : angle 2.07598 / 1.13 ( 12) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 296 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6822 (ttm110) REVERT: A 16 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8199 (mm) REVERT: A 86 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7680 (ttmm) REVERT: A 95 LYS cc_start: 0.8588 (mttp) cc_final: 0.8258 (mttp) REVERT: A 103 ASN cc_start: 0.8453 (m-40) cc_final: 0.8235 (m-40) REVERT: A 120 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7417 (p0) REVERT: A 125 LYS cc_start: 0.8119 (ttpt) cc_final: 0.7690 (tttt) REVERT: A 145 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8075 (ttpp) REVERT: A 181 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7287 (mt-10) REVERT: B 10 LYS cc_start: 0.8782 (mttp) cc_final: 0.8519 (mttp) REVERT: B 18 GLN cc_start: 0.7673 (mp10) cc_final: 0.7335 (mm110) REVERT: B 31 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7836 (mp) REVERT: B 78 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7689 (mp) REVERT: B 145 LYS cc_start: 0.8030 (tttt) cc_final: 0.7706 (ttmm) REVERT: B 152 TYR cc_start: 0.8808 (t80) cc_final: 0.8574 (t80) REVERT: B 170 ARG cc_start: 0.6981 (mtm-85) cc_final: 0.5668 (mpp-170) REVERT: C 74 ARG cc_start: 0.7916 (ttp-110) cc_final: 0.7532 (ptm-80) REVERT: C 119 GLU cc_start: 0.8525 (pp20) cc_final: 0.7954 (pp20) REVERT: C 200 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7557 (mmm-85) REVERT: C 299 LYS cc_start: 0.7154 (tttp) cc_final: 0.6867 (mtpt) REVERT: C 369 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7245 (tmt) REVERT: C 377 THR cc_start: 0.7619 (p) cc_final: 0.7401 (t) REVERT: C 407 ARG cc_start: 0.7823 (tpp80) cc_final: 0.7168 (mtm-85) REVERT: C 446 ASP cc_start: 0.8292 (p0) cc_final: 0.8006 (m-30) REVERT: C 470 ARG cc_start: 0.7279 (mtt-85) cc_final: 0.6897 (mtm-85) REVERT: C 479 LEU cc_start: 0.6745 (mt) cc_final: 0.6455 (mt) REVERT: C 492 MET cc_start: 0.8265 (mtp) cc_final: 0.7917 (mtp) REVERT: C 503 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7725 (mtpm) REVERT: C 515 MET cc_start: 0.8835 (ttp) cc_final: 0.8439 (ttm) REVERT: C 529 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7047 (tpm170) REVERT: C 540 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7858 (ptp-170) REVERT: C 582 ASN cc_start: 0.7782 (t0) cc_final: 0.7571 (t160) REVERT: C 641 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7427 (pp20) REVERT: C 719 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7233 (mmtt) REVERT: C 954 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7727 (mttp) REVERT: C 958 LYS cc_start: 0.6802 (tttt) cc_final: 0.6549 (tttp) REVERT: C 1034 ARG cc_start: 0.8188 (ptm-80) cc_final: 0.7863 (ttm-80) REVERT: D 60 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8268 (ttp-170) REVERT: D 200 GLN cc_start: 0.7123 (tt0) cc_final: 0.6761 (tm-30) REVERT: D 322 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.7938 (ttp80) REVERT: D 372 MET cc_start: 0.8773 (mtp) cc_final: 0.8452 (ttp) REVERT: D 375 GLU cc_start: 0.8486 (tp30) cc_final: 0.8127 (mm-30) REVERT: D 386 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7150 (mt-10) REVERT: D 443 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8343 (mt-10) REVERT: D 525 MET cc_start: 0.8458 (ptp) cc_final: 0.7892 (ptm) REVERT: D 649 LYS cc_start: 0.7050 (mmmt) cc_final: 0.6719 (mmtt) REVERT: D 704 GLU cc_start: 0.5302 (OUTLIER) cc_final: 0.4589 (tm-30) REVERT: D 712 GLN cc_start: 0.6759 (mt0) cc_final: 0.6277 (mm-40) REVERT: D 715 LYS cc_start: 0.8942 (ptmt) cc_final: 0.8421 (mtpt) REVERT: D 724 MET cc_start: 0.8155 (mtm) cc_final: 0.7770 (mtm) REVERT: D 743 MET cc_start: 0.8518 (ptp) cc_final: 0.8160 (ptp) REVERT: D 792 ASN cc_start: 0.7572 (t0) cc_final: 0.7341 (m110) REVERT: D 827 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7587 (mt-10) REVERT: D 873 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5640 (mp0) REVERT: D 1149 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6584 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7324 (ttm170) cc_final: 0.6450 (tmt90) REVERT: D 1188 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7116 (mm-30) REVERT: D 1189 MET cc_start: 0.8059 (mmp) cc_final: 0.7808 (mmp) REVERT: D 1193 TRP cc_start: 0.7834 (p-90) cc_final: 0.7625 (p90) REVERT: D 1205 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7651 (mp0) REVERT: D 1208 ASP cc_start: 0.8104 (m-30) cc_final: 0.7646 (m-30) REVERT: D 1260 MET cc_start: 0.8906 (mtp) cc_final: 0.8651 (mtm) REVERT: D 1372 ARG cc_start: 0.6574 (mmt180) cc_final: 0.5263 (tmm-80) REVERT: E 35 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6726 (mtmm) REVERT: E 67 ARG cc_start: 0.7100 (tpt170) cc_final: 0.6415 (mtp-110) REVERT: E 70 GLN cc_start: 0.7062 (tt0) cc_final: 0.6528 (tm-30) REVERT: F 131 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6737 (tm-30) REVERT: F 413 MET cc_start: 0.7057 (mtp) cc_final: 0.6812 (mtm) REVERT: F 485 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: F 567 MET cc_start: 0.8641 (mtt) cc_final: 0.8283 (mtm) REVERT: F 578 LYS cc_start: 0.7773 (mttt) cc_final: 0.7541 (mttt) outliers start: 84 outliers final: 29 residues processed: 353 average time/residue: 0.7546 time to fit residues: 310.3282 Evaluate side-chains 322 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 279 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 540 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 485 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [60, 323, 48, 130, 346, 325, 303, 113, 182, 213, 330] chunk 60 optimal weight: 3.9990 chunk 323 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 346 optimal weight: 6.9990 chunk 325 optimal weight: 0.6980 chunk 303 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN C 20 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.162380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099431 restraints weight = 39386.456| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.19 r_work: 0.3118 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 31820 Z= 0.257 Angle : 0.621 12.098 43413 Z= 0.325 Chirality : 0.046 0.242 4958 Planarity : 0.005 0.075 5300 Dihedral : 15.993 140.303 5143 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.08 % Allowed : 16.33 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -0.66 (0.14), residues: 3661 helix: 0.51 (0.14), residues: 1470 sheet: -1.35 (0.26), residues: 374 loop : -0.98 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 33 TYR 0.015 0.002 TYR C1281 PHE 0.029 0.002 PHE F 266 TRP 0.013 0.002 TRP D1193 HIS 0.008 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.26 (31811) covalent geometry : angle 0.61993 / 0.32 (43401) hydrogen bonds : bond 0.04160 / 2.80 ( 1376) hydrogen bonds : angle 4.54457 / 3.15 ( 3768) metal coordination : bond 0.00987 / 0.50 ( 8) metal coordination : angle 2.29908 / 1.22 ( 12) Misc. bond : bond 0.00067 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 286 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6786 (ttm110) REVERT: A 86 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7687 (ttmm) REVERT: A 95 LYS cc_start: 0.8564 (mttp) cc_final: 0.8352 (mttp) REVERT: A 103 ASN cc_start: 0.8449 (m-40) cc_final: 0.8249 (m-40) REVERT: A 125 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7624 (tttt) REVERT: A 145 LYS cc_start: 0.8377 (ttpt) cc_final: 0.8088 (ttpp) REVERT: A 181 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7228 (mt-10) REVERT: B 7 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6960 (pp20) REVERT: B 10 LYS cc_start: 0.8704 (mttp) cc_final: 0.8393 (mttp) REVERT: B 78 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7625 (mp) REVERT: B 145 LYS cc_start: 0.7983 (tttt) cc_final: 0.7651 (ttmm) REVERT: B 152 TYR cc_start: 0.8750 (t80) cc_final: 0.8530 (t80) REVERT: B 170 ARG cc_start: 0.6861 (mtm-85) cc_final: 0.5502 (mpp-170) REVERT: C 74 ARG cc_start: 0.7841 (ttp-110) cc_final: 0.7579 (ptm-80) REVERT: C 119 GLU cc_start: 0.8500 (pp20) cc_final: 0.7925 (pp20) REVERT: C 200 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7521 (mmm-85) REVERT: C 299 LYS cc_start: 0.7116 (tttp) cc_final: 0.6765 (mtpt) REVERT: C 315 MET cc_start: 0.7412 (mmp) cc_final: 0.6733 (ptm) REVERT: C 369 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6969 (tmt) REVERT: C 377 THR cc_start: 0.7591 (p) cc_final: 0.7367 (t) REVERT: C 407 ARG cc_start: 0.7679 (tpp80) cc_final: 0.7167 (mtm-85) REVERT: C 470 ARG cc_start: 0.7274 (mtt-85) cc_final: 0.6868 (mtm-85) REVERT: C 479 LEU cc_start: 0.6730 (mt) cc_final: 0.6474 (mt) REVERT: C 492 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7951 (mtp) REVERT: C 503 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7673 (mtpm) REVERT: C 515 MET cc_start: 0.8926 (ttp) cc_final: 0.8519 (ttm) REVERT: C 529 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6985 (tpm170) REVERT: C 540 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7940 (ptp-170) REVERT: C 582 ASN cc_start: 0.7928 (t0) cc_final: 0.7725 (t160) REVERT: C 719 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7135 (mmtt) REVERT: C 954 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7695 (mttp) REVERT: C 958 LYS cc_start: 0.6764 (tttt) cc_final: 0.6528 (tttp) REVERT: C 1020 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6658 (tm-30) REVERT: D 60 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8297 (ttp-170) REVERT: D 151 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8176 (mmm) REVERT: D 200 GLN cc_start: 0.7081 (tt0) cc_final: 0.6730 (tm-30) REVERT: D 322 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.7839 (ttp80) REVERT: D 372 MET cc_start: 0.8733 (mtp) cc_final: 0.8398 (ttp) REVERT: D 375 GLU cc_start: 0.8473 (tp30) cc_final: 0.8010 (tp30) REVERT: D 386 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7152 (mt-10) REVERT: D 443 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8235 (mt-10) REVERT: D 525 MET cc_start: 0.8655 (ptp) cc_final: 0.8000 (ptm) REVERT: D 649 LYS cc_start: 0.7085 (mmmt) cc_final: 0.6788 (mmtt) REVERT: D 704 GLU cc_start: 0.5611 (OUTLIER) cc_final: 0.4846 (tm-30) REVERT: D 712 GLN cc_start: 0.6643 (mt0) cc_final: 0.6245 (mm-40) REVERT: D 715 LYS cc_start: 0.8960 (ptmt) cc_final: 0.8393 (mtpt) REVERT: D 724 MET cc_start: 0.8110 (mtm) cc_final: 0.7706 (mtm) REVERT: D 743 MET cc_start: 0.8689 (ptp) cc_final: 0.8440 (ptp) REVERT: D 792 ASN cc_start: 0.7605 (t0) cc_final: 0.7302 (m110) REVERT: D 827 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7559 (mt-10) REVERT: D 901 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7071 (ttm170) REVERT: D 1149 ARG cc_start: 0.7176 (ttm-80) cc_final: 0.6532 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7282 (ttm170) cc_final: 0.6930 (ttp-170) REVERT: D 1205 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7643 (mp0) REVERT: D 1208 ASP cc_start: 0.8118 (m-30) cc_final: 0.7653 (m-30) REVERT: D 1260 MET cc_start: 0.8879 (mtp) cc_final: 0.8623 (mtm) REVERT: D 1372 ARG cc_start: 0.6541 (mmt180) cc_final: 0.5241 (tmm-80) REVERT: E 35 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7121 (mtmm) REVERT: E 67 ARG cc_start: 0.7172 (tpt170) cc_final: 0.6524 (mtp-110) REVERT: E 70 GLN cc_start: 0.6712 (tt0) cc_final: 0.6215 (tm-30) REVERT: F 131 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: F 413 MET cc_start: 0.7237 (mtp) cc_final: 0.6978 (mtm) REVERT: F 481 GLU cc_start: 0.8554 (tt0) cc_final: 0.8311 (tt0) REVERT: F 485 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: F 567 MET cc_start: 0.8442 (mtt) cc_final: 0.8145 (mtm) REVERT: F 578 LYS cc_start: 0.7742 (mttt) cc_final: 0.7442 (mptt) outliers start: 97 outliers final: 44 residues processed: 350 average time/residue: 0.7641 time to fit residues: 310.7508 Evaluate side-chains 333 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 276 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 540 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 558 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [104, 361, 67, 218, 125, 29, 199, 353, 226, 274, 308] chunk 104 optimal weight: 2.9990 chunk 361 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 218 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 199 optimal weight: 0.9990 chunk 353 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 chunk 274 optimal weight: 10.0000 chunk 308 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.164987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102392 restraints weight = 39355.154| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.20 r_work: 0.3175 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31820 Z= 0.127 Angle : 0.550 9.796 43413 Z= 0.291 Chirality : 0.042 0.243 4958 Planarity : 0.004 0.059 5300 Dihedral : 15.905 140.182 5143 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.19 % Allowed : 17.44 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -0.36 (0.14), residues: 3661 helix: 0.80 (0.14), residues: 1459 sheet: -1.26 (0.26), residues: 379 loop : -0.82 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 133 TYR 0.015 0.001 TYR F 137 PHE 0.014 0.001 PHE C 337 TRP 0.013 0.001 TRP D1193 HIS 0.005 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (31811) covalent geometry : angle 0.54865 / 0.29 (43401) hydrogen bonds : bond 0.03553 / 2.37 ( 1376) hydrogen bonds : angle 4.36824 / 3.02 ( 3768) metal coordination : bond 0.00448 / 0.22 ( 8) metal coordination : angle 1.98821 / 1.08 ( 12) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 284 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6786 (ttm110) REVERT: A 86 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7683 (ttmm) REVERT: A 103 ASN cc_start: 0.8471 (m-40) cc_final: 0.8251 (m-40) REVERT: A 125 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7657 (tttt) REVERT: A 145 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8121 (ttpp) REVERT: A 181 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7234 (mt-10) REVERT: B 10 LYS cc_start: 0.8755 (mttp) cc_final: 0.8490 (mttp) REVERT: B 31 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7814 (mp) REVERT: B 78 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7662 (mp) REVERT: B 145 LYS cc_start: 0.8083 (tttt) cc_final: 0.7735 (ttmm) REVERT: B 152 TYR cc_start: 0.8857 (t80) cc_final: 0.8626 (t80) REVERT: B 170 ARG cc_start: 0.6872 (mtm-85) cc_final: 0.5511 (mpp-170) REVERT: C 74 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7541 (ptm-80) REVERT: C 119 GLU cc_start: 0.8529 (pp20) cc_final: 0.7946 (pp20) REVERT: C 200 ARG cc_start: 0.8319 (mmm160) cc_final: 0.7528 (mmm-85) REVERT: C 299 LYS cc_start: 0.7203 (tttp) cc_final: 0.6858 (mtpt) REVERT: C 315 MET cc_start: 0.7444 (mmp) cc_final: 0.6756 (ptm) REVERT: C 369 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7324 (tmt) REVERT: C 377 THR cc_start: 0.7597 (p) cc_final: 0.7382 (t) REVERT: C 407 ARG cc_start: 0.7656 (tpp80) cc_final: 0.7159 (mtm-85) REVERT: C 446 ASP cc_start: 0.8315 (p0) cc_final: 0.7999 (m-30) REVERT: C 470 ARG cc_start: 0.7176 (mtt-85) cc_final: 0.6798 (mtm-85) REVERT: C 479 LEU cc_start: 0.6546 (mt) cc_final: 0.6267 (mt) REVERT: C 492 MET cc_start: 0.8239 (mtp) cc_final: 0.7894 (mtp) REVERT: C 503 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7721 (mtpm) REVERT: C 515 MET cc_start: 0.8848 (ttp) cc_final: 0.8458 (ttm) REVERT: C 529 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7047 (tpm170) REVERT: C 540 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7901 (ptp-170) REVERT: C 582 ASN cc_start: 0.7798 (t0) cc_final: 0.7590 (t160) REVERT: C 641 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7354 (pp20) REVERT: C 719 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7225 (mmtt) REVERT: C 954 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7733 (mttp) REVERT: C 958 LYS cc_start: 0.6801 (tttt) cc_final: 0.6555 (tttp) REVERT: C 1020 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6791 (tm-30) REVERT: C 1034 ARG cc_start: 0.8182 (ptm-80) cc_final: 0.7863 (ttm-80) REVERT: D 60 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8305 (ttp-170) REVERT: D 151 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8162 (mmm) REVERT: D 200 GLN cc_start: 0.7195 (tt0) cc_final: 0.6792 (tm-30) REVERT: D 322 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8030 (mtm110) REVERT: D 372 MET cc_start: 0.8687 (mtp) cc_final: 0.8397 (ttp) REVERT: D 375 GLU cc_start: 0.8490 (tp30) cc_final: 0.8139 (mm-30) REVERT: D 386 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7172 (mt-10) REVERT: D 388 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8380 (mmm-85) REVERT: D 443 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8258 (mt-10) REVERT: D 525 MET cc_start: 0.8536 (ptp) cc_final: 0.7987 (ptm) REVERT: D 649 LYS cc_start: 0.7191 (mmmt) cc_final: 0.6878 (mmtt) REVERT: D 704 GLU cc_start: 0.5418 (OUTLIER) cc_final: 0.4725 (tm-30) REVERT: D 712 GLN cc_start: 0.6664 (mt0) cc_final: 0.6244 (mm-40) REVERT: D 715 LYS cc_start: 0.8952 (ptmt) cc_final: 0.8432 (mtpt) REVERT: D 724 MET cc_start: 0.8129 (mtm) cc_final: 0.7730 (mtm) REVERT: D 827 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7582 (mt-10) REVERT: D 1149 ARG cc_start: 0.7157 (ttm-80) cc_final: 0.6575 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7339 (ttm170) cc_final: 0.6931 (ttp-170) REVERT: D 1188 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7576 (mm-30) REVERT: D 1205 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7635 (mp0) REVERT: D 1208 ASP cc_start: 0.8077 (m-30) cc_final: 0.7603 (m-30) REVERT: D 1260 MET cc_start: 0.8901 (mtp) cc_final: 0.8633 (mtm) REVERT: D 1372 ARG cc_start: 0.6569 (mmt180) cc_final: 0.5255 (tmm-80) REVERT: E 35 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6800 (mtmm) REVERT: E 67 ARG cc_start: 0.7186 (tpt170) cc_final: 0.6535 (mtp-110) REVERT: E 70 GLN cc_start: 0.7040 (tt0) cc_final: 0.6484 (tm-30) REVERT: F 131 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: F 322 MET cc_start: 0.4212 (tpt) cc_final: 0.3184 (ppp) REVERT: F 413 MET cc_start: 0.7354 (mtp) cc_final: 0.7097 (mtm) REVERT: F 481 GLU cc_start: 0.8442 (tt0) cc_final: 0.8190 (mt-10) REVERT: F 485 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: F 567 MET cc_start: 0.8437 (mtt) cc_final: 0.8200 (mtm) REVERT: F 578 LYS cc_start: 0.7726 (mttt) cc_final: 0.7441 (mptt) outliers start: 69 outliers final: 28 residues processed: 329 average time/residue: 0.7750 time to fit residues: 295.5116 Evaluate side-chains 317 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 540 ARG Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 485 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [296, 305, 157, 110, 263, 40, 326, 262, 176, 65, 171] chunk 296 optimal weight: 0.9980 chunk 305 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 326 optimal weight: 30.0000 chunk 262 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 65 optimal weight: 0.0010 chunk 171 optimal weight: 2.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN F 309 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.164655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.101888 restraints weight = 39193.503| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.20 r_work: 0.3138 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31820 Z= 0.148 Angle : 0.557 9.555 43413 Z= 0.293 Chirality : 0.043 0.239 4958 Planarity : 0.004 0.063 5300 Dihedral : 15.861 139.949 5143 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.09 % Allowed : 18.01 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3661 helix: 0.86 (0.14), residues: 1467 sheet: -1.18 (0.26), residues: 379 loop : -0.76 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 133 TYR 0.013 0.001 TYR C1281 PHE 0.031 0.001 PHE C 337 TRP 0.006 0.001 TRP F 326 HIS 0.004 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (31811) covalent geometry : angle 0.55614 / 0.29 (43401) hydrogen bonds : bond 0.03579 / 2.39 ( 1376) hydrogen bonds : angle 4.33422 / 2.99 ( 3768) metal coordination : bond 0.00544 / 0.27 ( 8) metal coordination : angle 1.93405 / 1.04 ( 12) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 283 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6717 (ttm110) REVERT: A 86 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7614 (ttmm) REVERT: A 103 ASN cc_start: 0.8416 (m-40) cc_final: 0.8203 (m-40) REVERT: A 125 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7594 (tttt) REVERT: A 145 LYS cc_start: 0.8343 (ttpt) cc_final: 0.8056 (ttpp) REVERT: A 181 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7182 (mt-10) REVERT: B 10 LYS cc_start: 0.8701 (mttp) cc_final: 0.8433 (mttp) REVERT: B 31 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7752 (mp) REVERT: B 78 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7605 (mp) REVERT: B 145 LYS cc_start: 0.8000 (tttt) cc_final: 0.7659 (ttmm) REVERT: B 152 TYR cc_start: 0.8824 (t80) cc_final: 0.8604 (t80) REVERT: B 170 ARG cc_start: 0.6880 (mtm-85) cc_final: 0.5502 (mpp-170) REVERT: C 74 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7498 (ptm-80) REVERT: C 119 GLU cc_start: 0.8513 (pp20) cc_final: 0.7927 (pp20) REVERT: C 200 ARG cc_start: 0.8294 (mmm160) cc_final: 0.7517 (mmm-85) REVERT: C 299 LYS cc_start: 0.7166 (tttp) cc_final: 0.6831 (mtpt) REVERT: C 315 MET cc_start: 0.7412 (mmp) cc_final: 0.6724 (ptm) REVERT: C 369 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7269 (tmt) REVERT: C 377 THR cc_start: 0.7517 (p) cc_final: 0.7302 (t) REVERT: C 407 ARG cc_start: 0.7631 (tpp80) cc_final: 0.7114 (mtm-85) REVERT: C 446 ASP cc_start: 0.8167 (p0) cc_final: 0.7948 (m-30) REVERT: C 470 ARG cc_start: 0.7145 (mtt-85) cc_final: 0.6752 (mtm-85) REVERT: C 479 LEU cc_start: 0.6090 (mt) cc_final: 0.5757 (mt) REVERT: C 492 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7878 (mtp) REVERT: C 503 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7680 (mtpm) REVERT: C 510 GLN cc_start: 0.8240 (tt0) cc_final: 0.7633 (tp40) REVERT: C 515 MET cc_start: 0.8844 (ttp) cc_final: 0.8460 (ttm) REVERT: C 529 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6905 (tpm170) REVERT: C 540 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7860 (ptp-170) REVERT: C 641 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7323 (pp20) REVERT: C 719 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7150 (mmtt) REVERT: C 954 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7685 (mttp) REVERT: C 958 LYS cc_start: 0.6741 (tttt) cc_final: 0.6504 (tttp) REVERT: C 1020 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6753 (tm-30) REVERT: C 1034 ARG cc_start: 0.8152 (ptm-80) cc_final: 0.7829 (ttm-80) REVERT: D 60 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8279 (ttp-170) REVERT: D 147 ILE cc_start: 0.8079 (mt) cc_final: 0.7667 (mp) REVERT: D 151 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8161 (mmm) REVERT: D 200 GLN cc_start: 0.7150 (tt0) cc_final: 0.6750 (tm-30) REVERT: D 322 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7934 (ttp80) REVERT: D 372 MET cc_start: 0.8659 (mtp) cc_final: 0.8364 (ttp) REVERT: D 375 GLU cc_start: 0.8457 (tp30) cc_final: 0.8093 (mm-30) REVERT: D 386 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7138 (mt-10) REVERT: D 388 ARG cc_start: 0.8519 (mmm-85) cc_final: 0.8285 (mmm-85) REVERT: D 443 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8252 (mt-10) REVERT: D 525 MET cc_start: 0.8525 (ptp) cc_final: 0.7955 (ptm) REVERT: D 649 LYS cc_start: 0.7147 (mmmt) cc_final: 0.6826 (mmtt) REVERT: D 704 GLU cc_start: 0.5437 (OUTLIER) cc_final: 0.4732 (tm-30) REVERT: D 712 GLN cc_start: 0.6626 (mt0) cc_final: 0.6182 (mm-40) REVERT: D 715 LYS cc_start: 0.8939 (ptmt) cc_final: 0.8399 (mtpt) REVERT: D 724 MET cc_start: 0.8051 (mtm) cc_final: 0.7654 (mtm) REVERT: D 792 ASN cc_start: 0.7534 (t0) cc_final: 0.7263 (m110) REVERT: D 827 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7558 (mt-10) REVERT: D 873 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5446 (mp0) REVERT: D 1060 VAL cc_start: 0.3510 (OUTLIER) cc_final: 0.2921 (t) REVERT: D 1149 ARG cc_start: 0.7146 (ttm-80) cc_final: 0.6494 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7242 (ttm170) cc_final: 0.6859 (ttp-170) REVERT: D 1205 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7637 (mp0) REVERT: D 1208 ASP cc_start: 0.8022 (m-30) cc_final: 0.7563 (m-30) REVERT: D 1260 MET cc_start: 0.8870 (mtp) cc_final: 0.8606 (mtm) REVERT: D 1372 ARG cc_start: 0.6526 (mmt180) cc_final: 0.5224 (tmm-80) REVERT: E 35 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.6806 (mtmm) REVERT: E 67 ARG cc_start: 0.7164 (tpt170) cc_final: 0.6510 (mtp-110) REVERT: E 70 GLN cc_start: 0.6696 (tt0) cc_final: 0.6236 (tm-30) REVERT: F 131 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: F 322 MET cc_start: 0.4180 (tpt) cc_final: 0.3191 (ppp) REVERT: F 413 MET cc_start: 0.7296 (mtp) cc_final: 0.7031 (mtm) REVERT: F 481 GLU cc_start: 0.8454 (tt0) cc_final: 0.8223 (mt-10) REVERT: F 485 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: F 578 LYS cc_start: 0.7697 (mttt) cc_final: 0.7403 (mptt) outliers start: 66 outliers final: 33 residues processed: 327 average time/residue: 0.8025 time to fit residues: 308.2208 Evaluate side-chains 325 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 276 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 540 ARG Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 485 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [344, 90, 1, 298, 233, 93, 142, 13, 86, 291, 60] chunk 344 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 298 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 291 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 129 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098605 restraints weight = 39423.439| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.18 r_work: 0.3092 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 31820 Z= 0.307 Angle : 0.665 9.415 43413 Z= 0.345 Chirality : 0.048 0.243 4958 Planarity : 0.005 0.073 5300 Dihedral : 15.965 139.962 5143 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.47 % Allowed : 18.05 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -0.57 (0.14), residues: 3661 helix: 0.54 (0.14), residues: 1476 sheet: -1.25 (0.27), residues: 379 loop : -0.91 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 133 TYR 0.015 0.002 TYR C1281 PHE 0.017 0.002 PHE D 437 TRP 0.009 0.002 TRP C1276 HIS 0.009 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.31 (31811) covalent geometry : angle 0.66407 / 0.34 (43401) hydrogen bonds : bond 0.04275 / 2.88 ( 1376) hydrogen bonds : angle 4.54430 / 3.14 ( 3768) metal coordination : bond 0.01111 / 0.58 ( 8) metal coordination : angle 2.27491 / 1.19 ( 12) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 274 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6765 (ttm110) REVERT: A 86 LYS cc_start: 0.7761 (ttmt) cc_final: 0.7483 (ttmm) REVERT: A 103 ASN cc_start: 0.8426 (m-40) cc_final: 0.8206 (m-40) REVERT: A 125 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7632 (tttt) REVERT: A 145 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8013 (ttpp) REVERT: A 181 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7316 (mt-10) REVERT: B 10 LYS cc_start: 0.8775 (mttp) cc_final: 0.8487 (mttm) REVERT: B 78 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7689 (mp) REVERT: B 145 LYS cc_start: 0.8040 (tttt) cc_final: 0.7697 (ttmm) REVERT: B 152 TYR cc_start: 0.8789 (t80) cc_final: 0.8584 (t80) REVERT: B 170 ARG cc_start: 0.6905 (mtm-85) cc_final: 0.5574 (mpp-170) REVERT: C 74 ARG cc_start: 0.7786 (ttp-110) cc_final: 0.7576 (ptm-80) REVERT: C 119 GLU cc_start: 0.8508 (pp20) cc_final: 0.8025 (pp20) REVERT: C 200 ARG cc_start: 0.8327 (mmm160) cc_final: 0.7521 (mmm-85) REVERT: C 299 LYS cc_start: 0.7197 (tttp) cc_final: 0.6867 (mtpt) REVERT: C 315 MET cc_start: 0.7416 (mmp) cc_final: 0.6678 (ptp) REVERT: C 369 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.6985 (tmt) REVERT: C 377 THR cc_start: 0.7563 (p) cc_final: 0.7336 (t) REVERT: C 407 ARG cc_start: 0.7702 (tpp80) cc_final: 0.7178 (mtm-85) REVERT: C 470 ARG cc_start: 0.7221 (mtt-85) cc_final: 0.6812 (mtm-85) REVERT: C 479 LEU cc_start: 0.6557 (mt) cc_final: 0.6311 (mt) REVERT: C 492 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7959 (mtp) REVERT: C 496 LYS cc_start: 0.7567 (mmmm) cc_final: 0.6924 (tmmt) REVERT: C 503 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7678 (mtpm) REVERT: C 515 MET cc_start: 0.8962 (ttp) cc_final: 0.8562 (ttm) REVERT: C 529 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7038 (tpm170) REVERT: C 719 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7154 (mmtt) REVERT: C 954 LYS cc_start: 0.7965 (mtpt) cc_final: 0.7694 (mttp) REVERT: C 958 LYS cc_start: 0.6776 (tttt) cc_final: 0.6540 (tttp) REVERT: C 1020 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: C 1088 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8352 (p0) REVERT: D 60 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8321 (ttp-170) REVERT: D 147 ILE cc_start: 0.8095 (mt) cc_final: 0.7696 (mp) REVERT: D 200 GLN cc_start: 0.7218 (tt0) cc_final: 0.6808 (tm-30) REVERT: D 322 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7900 (ttp80) REVERT: D 372 MET cc_start: 0.8733 (mtp) cc_final: 0.8397 (ttp) REVERT: D 375 GLU cc_start: 0.8490 (tp30) cc_final: 0.8025 (tp30) REVERT: D 388 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.8264 (mmm-85) REVERT: D 443 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8111 (mt-10) REVERT: D 649 LYS cc_start: 0.7237 (mmmt) cc_final: 0.6951 (mmtt) REVERT: D 704 GLU cc_start: 0.5671 (OUTLIER) cc_final: 0.4898 (tm-30) REVERT: D 712 GLN cc_start: 0.6695 (mt0) cc_final: 0.6249 (mm-40) REVERT: D 715 LYS cc_start: 0.8975 (ptmt) cc_final: 0.8398 (mtpt) REVERT: D 724 MET cc_start: 0.8118 (mtm) cc_final: 0.7740 (mtm) REVERT: D 827 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7614 (mt-10) REVERT: D 873 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5476 (mp0) REVERT: D 1149 ARG cc_start: 0.7195 (ttm-80) cc_final: 0.6559 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7336 (ttm170) cc_final: 0.6946 (ttp-170) REVERT: D 1205 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7607 (mp0) REVERT: D 1208 ASP cc_start: 0.8027 (m-30) cc_final: 0.7508 (m-30) REVERT: D 1260 MET cc_start: 0.8898 (mtp) cc_final: 0.8635 (mtm) REVERT: D 1372 ARG cc_start: 0.6567 (mmt180) cc_final: 0.5257 (tmm-80) REVERT: E 35 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7149 (mtmm) REVERT: E 67 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6532 (mtp-110) REVERT: E 70 GLN cc_start: 0.6765 (tt0) cc_final: 0.6308 (tm-30) REVERT: F 102 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7177 (mmt) REVERT: F 131 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: F 322 MET cc_start: 0.4058 (tpt) cc_final: 0.3195 (ppp) REVERT: F 481 GLU cc_start: 0.8369 (tt0) cc_final: 0.8082 (mt-10) REVERT: F 485 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: F 578 LYS cc_start: 0.7651 (mttt) cc_final: 0.7436 (mttt) outliers start: 78 outliers final: 44 residues processed: 330 average time/residue: 0.7724 time to fit residues: 296.4394 Evaluate side-chains 323 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 266 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1088 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 527 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [7, 123, 190, 336, 138, 81, 62, 231, 254, 32, 278] chunk 7 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 336 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 278 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.164853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.102221 restraints weight = 39205.590| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.20 r_work: 0.3142 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31820 Z= 0.121 Angle : 0.571 9.943 43413 Z= 0.299 Chirality : 0.043 0.243 4958 Planarity : 0.004 0.066 5300 Dihedral : 15.869 139.811 5143 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.59 % Allowed : 19.19 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: -0.24 (0.14), residues: 3661 helix: 0.88 (0.14), residues: 1456 sheet: -1.15 (0.27), residues: 379 loop : -0.74 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 133 TYR 0.021 0.001 TYR D1186 PHE 0.027 0.001 PHE F 266 TRP 0.010 0.001 TRP C 807 HIS 0.004 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (31811) covalent geometry : angle 0.57063 / 0.30 (43401) hydrogen bonds : bond 0.03535 / 2.36 ( 1376) hydrogen bonds : angle 4.35480 / 3.00 ( 3768) metal coordination : bond 0.00411 / 0.21 ( 8) metal coordination : angle 1.86021 / 1.00 ( 12) Misc. bond : bond 0.00019 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 279 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6720 (ttm110) REVERT: A 86 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7637 (ttmm) REVERT: A 103 ASN cc_start: 0.8423 (m-40) cc_final: 0.8208 (m-40) REVERT: A 125 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7588 (tttt) REVERT: A 145 LYS cc_start: 0.8284 (ttpt) cc_final: 0.7978 (ttpp) REVERT: A 181 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7183 (mt-10) REVERT: B 10 LYS cc_start: 0.8690 (mttp) cc_final: 0.8376 (mttm) REVERT: B 78 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7582 (mp) REVERT: B 145 LYS cc_start: 0.8010 (tttt) cc_final: 0.7752 (ttmm) REVERT: B 152 TYR cc_start: 0.8828 (t80) cc_final: 0.8595 (t80) REVERT: B 170 ARG cc_start: 0.6872 (mtm-85) cc_final: 0.5494 (mpp-170) REVERT: C 74 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7508 (ptm-80) REVERT: C 119 GLU cc_start: 0.8506 (pp20) cc_final: 0.7917 (pp20) REVERT: C 200 ARG cc_start: 0.8302 (mmm160) cc_final: 0.7496 (mmm-85) REVERT: C 299 LYS cc_start: 0.7192 (tttp) cc_final: 0.6865 (mtpt) REVERT: C 315 MET cc_start: 0.7415 (mmp) cc_final: 0.6684 (ptp) REVERT: C 369 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7241 (tmt) REVERT: C 377 THR cc_start: 0.7547 (p) cc_final: 0.7330 (t) REVERT: C 407 ARG cc_start: 0.7626 (tpp80) cc_final: 0.7109 (mtm-85) REVERT: C 446 ASP cc_start: 0.8011 (p0) cc_final: 0.7808 (m-30) REVERT: C 470 ARG cc_start: 0.7120 (mtt-85) cc_final: 0.6733 (mtm-85) REVERT: C 479 LEU cc_start: 0.6200 (mt) cc_final: 0.5878 (mt) REVERT: C 492 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7943 (mtp) REVERT: C 496 LYS cc_start: 0.7530 (mmmm) cc_final: 0.6898 (tmmt) REVERT: C 503 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7650 (mtpm) REVERT: C 510 GLN cc_start: 0.8171 (tt0) cc_final: 0.7585 (tp40) REVERT: C 515 MET cc_start: 0.8841 (ttp) cc_final: 0.8454 (ttm) REVERT: C 529 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6956 (tpm170) REVERT: C 625 GLU cc_start: 0.7939 (tp30) cc_final: 0.7694 (tp30) REVERT: C 719 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7198 (mmtt) REVERT: C 779 ARG cc_start: 0.8464 (ttt-90) cc_final: 0.7762 (ttm110) REVERT: C 954 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7685 (mttp) REVERT: C 958 LYS cc_start: 0.6741 (tttt) cc_final: 0.6506 (tttp) REVERT: C 1020 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: C 1034 ARG cc_start: 0.8138 (ptm-80) cc_final: 0.7826 (ttm-80) REVERT: D 60 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8275 (ttp-170) REVERT: D 147 ILE cc_start: 0.8079 (mt) cc_final: 0.7698 (mp) REVERT: D 200 GLN cc_start: 0.7185 (tt0) cc_final: 0.6776 (tm-30) REVERT: D 322 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.8032 (mtp85) REVERT: D 372 MET cc_start: 0.8627 (mtp) cc_final: 0.8334 (ttp) REVERT: D 375 GLU cc_start: 0.8447 (tp30) cc_final: 0.8067 (mm-30) REVERT: D 386 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7212 (mt-10) REVERT: D 388 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8340 (mmm-85) REVERT: D 525 MET cc_start: 0.8603 (ptp) cc_final: 0.8102 (ptm) REVERT: D 649 LYS cc_start: 0.7113 (mmmt) cc_final: 0.6825 (mmtt) REVERT: D 704 GLU cc_start: 0.5430 (OUTLIER) cc_final: 0.4725 (tm-30) REVERT: D 712 GLN cc_start: 0.6624 (mt0) cc_final: 0.6185 (mm-40) REVERT: D 715 LYS cc_start: 0.8954 (ptmt) cc_final: 0.8415 (mtpt) REVERT: D 724 MET cc_start: 0.8055 (mtm) cc_final: 0.7655 (mtm) REVERT: D 827 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7558 (mt-10) REVERT: D 873 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.5414 (mp0) REVERT: D 1060 VAL cc_start: 0.3500 (OUTLIER) cc_final: 0.2913 (t) REVERT: D 1149 ARG cc_start: 0.7145 (ttm-80) cc_final: 0.6550 (mtp-110) REVERT: D 1174 ARG cc_start: 0.7338 (ttm170) cc_final: 0.6949 (ttp-170) REVERT: D 1205 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7637 (mp0) REVERT: D 1208 ASP cc_start: 0.7988 (m-30) cc_final: 0.7556 (m-30) REVERT: D 1260 MET cc_start: 0.8874 (mtp) cc_final: 0.8633 (mtm) REVERT: D 1372 ARG cc_start: 0.6526 (mmt180) cc_final: 0.5222 (tmm-80) REVERT: E 35 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7029 (mtmm) REVERT: E 67 ARG cc_start: 0.7151 (tpt170) cc_final: 0.6498 (mtp-110) REVERT: E 70 GLN cc_start: 0.6744 (tt0) cc_final: 0.6280 (tm-30) REVERT: F 131 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: F 322 MET cc_start: 0.4055 (tpt) cc_final: 0.3183 (ppp) REVERT: F 413 MET cc_start: 0.7051 (mtm) cc_final: 0.6816 (mtm) REVERT: F 481 GLU cc_start: 0.8347 (tt0) cc_final: 0.8115 (mt-10) REVERT: F 485 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8059 (mp0) outliers start: 50 outliers final: 32 residues processed: 314 average time/residue: 0.7677 time to fit residues: 279.1003 Evaluate side-chains 314 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 270 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 873 GLU Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 485 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: [269, 73, 183, 196, 266, 23, 104, 62, 243, 52, 100] chunk 269 optimal weight: 0.0970 chunk 73 optimal weight: 20.0000 chunk 183 optimal weight: 0.0270 chunk 196 optimal weight: 0.8980 chunk 266 optimal weight: 4.9990 chunk 23 optimal weight: 0.0000 chunk 104 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 243 optimal weight: 0.0770 chunk 52 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.166635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.104687 restraints weight = 39279.647| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.19 r_work: 0.3192 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 31820 Z= 0.106 Angle : 0.549 11.559 43413 Z= 0.288 Chirality : 0.042 0.234 4958 Planarity : 0.004 0.066 5300 Dihedral : 15.746 139.276 5143 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.52 % Allowed : 19.35 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: 0.00 (0.14), residues: 3661 helix: 1.07 (0.14), residues: 1469 sheet: -1.02 (0.27), residues: 381 loop : -0.61 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 133 TYR 0.033 0.001 TYR D1186 PHE 0.030 0.001 PHE D 176 TRP 0.009 0.001 TRP C 807 HIS 0.015 0.001 HIS C 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (31811) covalent geometry : angle 0.54833 / 0.29 (43401) hydrogen bonds : bond 0.03305 / 2.19 ( 1376) hydrogen bonds : angle 4.22502 / 2.91 ( 3768) metal coordination : bond 0.00330 / 0.15 ( 8) metal coordination : angle 1.75071 / 0.96 ( 12) Misc. bond : bond 0.00030 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15411.93 seconds wall clock time: 261 minutes 19.89 seconds (15679.89 seconds total)