Starting phenix.real_space_refine on Tue Sep 15 05:25:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xl5_22234/09_2026/6xl5_22234.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xl5_22234/09_2026/6xl5_22234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xl5_22234/09_2026/6xl5_22234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xl5_22234/09_2026/6xl5_22234.map" model { file = "/net/cci-nas-00/data/ceres_data/6xl5_22234/09_2026/6xl5_22234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xl5_22234/09_2026/6xl5_22234.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xl5_22234/09_2026/6xl5_22234.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xl5_22234/09_2026/6xl5_22234.cif" } resolution = 2.5 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= 0.002 sd= 0.092 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: 8 Type Number sf(0) Gaussians Sb 2 10.97 5 Zn 2 6.06 5 P 106 5.49 5 Mg 1 5.21 5 S 155 5.16 5 C 22215 2.51 5 N 6272 2.21 5 O 7075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35828 Number of models: 1 Model: "" Number of chains: 20 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: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10394 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: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1109 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "T" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1104 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "G" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "H" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} 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} Chain: "T" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14523 SG CYS D 70 81.657 84.624 57.453 1.00 60.18 S ATOM 14537 SG CYS D 72 78.764 83.895 56.623 1.00 62.43 S ATOM 14645 SG CYS D 85 79.503 84.961 53.727 1.00 61.19 S ATOM 14669 SG CYS D 88 78.979 87.091 56.479 1.00 58.84 S ATOM 20357 SG CYS D 814 115.203 142.345 64.775 1.00 51.71 S ATOM 20922 SG CYS D 888 112.902 140.407 66.658 1.00 48.63 S ATOM 20973 SG CYS D 895 116.415 139.842 66.983 1.00 45.92 S ATOM 20994 SG CYS D 898 115.033 142.648 68.430 1.00 45.52 S Time building chain proxies: 7.82, per 1000 atoms: 0.22 Number of scatterers: 35828 At special positions: 0 Unit cell: (181.288, 209.725, 161.737, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Sb 2 50.95 Zn 2 29.99 S 155 16.00 P 106 15.00 Mg 1 11.99 O 7075 8.00 N 6272 7.00 C 22215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " Number of angles added : 12 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7868 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 56 sheets defined 44.0% alpha, 17.7% beta 40 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 5.70 Creating SS restraints... Processing helix chain 'A' and resid 34 through 48 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.752A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 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: 3.515A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.679A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.593A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.816A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.185A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 293' Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.565A pdb=" N SER C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) 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 389 removed outlier: 3.802A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.716A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.072A 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: 4.381A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.733A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix 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: 4.207A 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 738 through 741 Processing helix chain 'C' and resid 811 through 813 No H-bonds generated for 'chain 'C' and resid 811 through 813' Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.878A pdb=" N GLY C 982 " --> pdb=" O VAL C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1000 removed outlier: 3.520A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1038 removed outlier: 3.663A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU C1030 " --> pdb=" O GLU C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.533A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1109 through 1134 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 1238 through 1243 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: 3.827A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1331 removed outlier: 3.548A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.565A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.634A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 176 removed outlier: 4.459A pdb=" N PHE D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 206 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: 3.960A 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: 3.869A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.664A 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: 3.934A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.902A 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 485 through 489 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.811A 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 613 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.559A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.534A pdb=" N ASP D 643 " --> pdb=" O GLY D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.180A 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: 3.760A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 4.302A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.667A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.782A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.535A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1293 Processing helix chain 'D' and resid 1308 through 1314 removed outlier: 3.525A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.504A 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 1346 through 1353 removed outlier: 3.777A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (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 1372 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.909A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.695A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 60 through 78 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 112 through 135 removed outlier: 3.672A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.338A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 160 Processing helix chain 'F' and resid 213 through 233 removed outlier: 4.350A pdb=" N ALA F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 257 removed outlier: 4.335A pdb=" N GLU F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU F 250 " --> pdb=" O GLN F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 295 removed outlier: 3.935A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS F 295 " --> pdb=" O CYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.380A pdb=" N ASN F 309 " --> pdb=" O LEU F 305 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU F 310 " --> pdb=" O PHE F 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 305 through 310' Processing helix chain 'F' and resid 316 through 321 removed outlier: 4.345A pdb=" N ILE F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA F 321 " --> pdb=" O ASN F 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 316 through 321' Processing helix chain 'F' and resid 324 through 330 removed outlier: 3.565A pdb=" N GLU F 328 " --> pdb=" O LYS F 324 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS F 329 " --> pdb=" O PRO F 325 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU F 330 " --> pdb=" O TRP F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 324 through 330' Processing helix chain 'F' and resid 331 through 334 Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 343 through 352 removed outlier: 4.411A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 383 removed outlier: 3.585A pdb=" N ASN F 383 " --> pdb=" O MET F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 removed outlier: 3.516A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (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 419 Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.564A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 447 removed outlier: 3.746A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 Processing helix chain 'F' and resid 479 through 487 Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 510 through 514 removed outlier: 3.912A pdb=" N ASP F 514 " --> pdb=" O ILE F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.751A pdb=" N ILE F 523 " --> pdb=" O GLY F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 550 Processing helix chain 'F' and resid 552 through 563 removed outlier: 3.704A pdb=" N PHE F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 581 Processing helix chain 'F' and resid 583 through 600 removed outlier: 3.636A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS F 600 " --> pdb=" O ARG F 596 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 605 removed outlier: 3.829A pdb=" N GLU F 605 " --> pdb=" O PRO F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 611 Processing helix chain 'G' and resid 3 through 12 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.578A pdb=" N LEU G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 57 removed outlier: 3.900A pdb=" N LYS G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN G 51 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 107 removed outlier: 3.680A pdb=" N ILE G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 140 removed outlier: 3.951A pdb=" N ILE G 140 " --> pdb=" O PHE G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 154 removed outlier: 3.526A pdb=" N ILE G 146 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 233 removed outlier: 3.881A pdb=" N ALA G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 12 Processing helix chain 'H' and resid 14 through 25 Processing helix chain 'H' and resid 42 through 57 removed outlier: 3.705A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 removed outlier: 3.708A pdb=" N THR H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 109 removed outlier: 3.915A pdb=" N GLU H 79 " --> pdb=" O CYS H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 154 Proline residue: H 144 - end of helix Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 218 through 233 removed outlier: 4.127A pdb=" N ALA H 222 " --> pdb=" O SER H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 257 removed outlier: 3.577A pdb=" N GLU H 257 " --> pdb=" O ASP H 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 254 through 257' Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.105A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.518A 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: 5.713A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.535A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.498A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.720A 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: 6.212A 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: 6.328A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.474A 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: 3.716A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (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 111 removed outlier: 3.557A 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: 6.300A 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: 4.966A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.908A 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: 4.944A 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 301 through 302 Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.116A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.289A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.627A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 6.813A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.338A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.662A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.567A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 3.570A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.572A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.057A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.033A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD8, first strand: chain 'D' and resid 350 through 357 Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'D' and resid 705 through 709 removed outlier: 4.019A pdb=" N THR D 705 " --> pdb=" O GLN D 716 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.507A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.593A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.461A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 957 through 961 removed outlier: 6.578A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 4.131A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1098 through 1100 Processing sheet with id=AF1, first strand: chain 'D' and resid 1155 through 1156 removed outlier: 6.465A pdb=" N ILE D1155 " --> pdb=" O ILE D1210 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1187 through 1191 removed outlier: 3.505A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.762A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 162 through 165 removed outlier: 7.735A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 31 through 32 Processing sheet with id=AF6, first strand: chain 'G' and resid 117 through 121 removed outlier: 5.222A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 117 through 121 removed outlier: 5.222A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET G 259 " --> pdb=" O ILE G 246 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 165 through 169 removed outlier: 4.142A pdb=" N ILE G 125 " --> pdb=" O VAL G 187 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 31 through 32 Processing sheet with id=AG1, first strand: chain 'H' and resid 117 through 121 removed outlier: 5.176A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE H 125 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 117 through 121 removed outlier: 5.176A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) 1555 hydrogen bonds defined for protein. 4353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 12.40 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.39: 14344 1.39 - 1.58: 21765 1.58 - 1.76: 218 1.76 - 1.95: 263 1.95 - 2.13: 8 Bond restraints: 36598 Sorted by residual: bond pdb=" C1' DC T 15 " pdb=" N1 DC T 15 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.89e+01 bond pdb=" C3' DT N 77 " pdb=" O3' DT N 77 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.26e+01 bond pdb=" C3' DA T 21 " pdb=" O3' DA T 21 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.24e+01 bond pdb=" C3' DG N 60 " pdb=" O3' DG N 60 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.19e+01 bond pdb=" C3' DC N 42 " pdb=" O3' DC N 42 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.10e+01 ... (remaining 36593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 48732 2.61 - 5.22: 1088 5.22 - 7.82: 96 7.82 - 10.43: 14 10.43 - 13.04: 1 Bond angle restraints: 49931 Sorted by residual: angle pdb=" N ASP C1296 " pdb=" CA ASP C1296 " pdb=" C ASP C1296 " ideal model delta sigma weight residual 113.50 123.55 -10.05 1.23e+00 6.61e-01 6.67e+01 angle pdb=" N TYR G 114 " pdb=" CA TYR G 114 " pdb=" C TYR G 114 " ideal model delta sigma weight residual 107.70 120.74 -13.04 2.09e+00 2.29e-01 3.89e+01 angle pdb=" O5' DG N 59 " pdb=" C5' DG N 59 " pdb=" C4' DG N 59 " ideal model delta sigma weight residual 109.40 114.03 -4.63 8.00e-01 1.56e+00 3.34e+01 angle pdb=" N ASP D 505 " pdb=" CA ASP D 505 " pdb=" C ASP D 505 " ideal model delta sigma weight residual 111.33 117.76 -6.43 1.21e+00 6.83e-01 2.82e+01 angle pdb=" O4' DT N 61 " pdb=" C4' DT N 61 " pdb=" C3' DT N 61 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.64e+01 ... (remaining 49926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 21219 35.47 - 70.93: 834 70.93 - 106.40: 34 106.40 - 141.86: 0 141.86 - 177.33: 3 Dihedral angle restraints: 22090 sinusoidal: 9885 harmonic: 12205 Sorted by residual: dihedral pdb=" CA GLU F 154 " pdb=" C GLU F 154 " pdb=" N GLU F 155 " pdb=" CA GLU F 155 " ideal model delta harmonic sigma weight residual 180.00 150.96 29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA HIS A 160 " pdb=" C HIS A 160 " pdb=" N SER A 161 " pdb=" CA SER A 161 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU F 328 " pdb=" C GLU F 328 " pdb=" N LYS F 329 " pdb=" CA LYS F 329 " ideal model delta harmonic sigma weight residual 180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 22087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4487 0.072 - 0.145: 1067 0.145 - 0.217: 110 0.217 - 0.290: 12 0.290 - 0.362: 5 Chirality restraints: 5681 Sorted by residual: chirality pdb=" CA ASP C1296 " pdb=" N ASP C1296 " pdb=" C ASP C1296 " pdb=" CB ASP C1296 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CB VAL D1353 " pdb=" CA VAL D1353 " pdb=" CG1 VAL D1353 " pdb=" CG2 VAL D1353 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CB VAL C1293 " pdb=" CA VAL C1293 " pdb=" CG1 VAL C1293 " pdb=" CG2 VAL C1293 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 5678 not shown) Planarity restraints: 6095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE H 77 " -0.025 2.00e-02 2.50e+03 4.94e-02 2.44e+01 pdb=" C ILE H 77 " 0.086 2.00e-02 2.50e+03 pdb=" O ILE H 77 " -0.031 2.00e-02 2.50e+03 pdb=" N ILE H 78 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 79 " 0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" CD GLU G 79 " -0.076 2.00e-02 2.50e+03 pdb=" OE1 GLU G 79 " 0.027 2.00e-02 2.50e+03 pdb=" OE2 GLU G 79 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 221 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ASN G 221 " 0.066 2.00e-02 2.50e+03 pdb=" O ASN G 221 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA G 222 " -0.022 2.00e-02 2.50e+03 ... (remaining 6092 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 661 2.65 - 3.22: 32016 3.22 - 3.78: 58289 3.78 - 4.34: 82879 4.34 - 4.90: 133426 Nonbonded interactions: 307271 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.093 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 2.190 2.170 nonbonded pdb=" O GLY D 613 " pdb=" OG1 THR D 617 " model vdw 2.200 3.040 nonbonded pdb=" O THR D 816 " pdb=" NH2 ARG D 860 " model vdw 2.201 3.120 nonbonded pdb=" OE1 GLU D 993 " pdb=" OH TYR D 995 " model vdw 2.208 3.040 ... (remaining 307266 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) } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 2 through 269 or (resid 301 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 o \ r name O2 or name O3 or name O4 )) or resid 302)) } 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: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 49.580 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 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:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.011 0.205 36606 Z= 0.502 Angle : 0.976 38.694 49943 Z= 0.574 Chirality : 0.061 0.362 5681 Planarity : 0.006 0.063 6095 Dihedral : 16.987 177.330 14222 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.11), residues: 4194 helix: -1.82 (0.10), residues: 1636 sheet: -1.54 (0.20), residues: 513 loop : -1.50 (0.12), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 678 TYR 0.027 0.003 TYR G 164 PHE 0.024 0.003 PHE G 131 TRP 0.033 0.002 TRP H 250 HIS 0.025 0.002 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.01044 / 0.50 (36598) covalent geometry : angle 0.94692 / 0.57 (49931) hydrogen bonds : bond 0.15107 / 10.10 ( 1632) hydrogen bonds : angle 6.94499 / 4.84 ( 4567) metal coordination : bond 0.12437 / 5.88 ( 8) metal coordination : angle 15.33864 / 8.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: B 104 LYS cc_start: 0.7691 (tptm) cc_final: 0.7416 (tptp) REVERT: C 118 LYS cc_start: 0.8483 (mttm) cc_final: 0.8001 (ttmt) REVERT: C 240 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6446 (mm-30) REVERT: C 386 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 488 MET cc_start: 0.7761 (mmm) cc_final: 0.7149 (mmm) REVERT: C 496 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7596 (tttp) REVERT: C 834 GLN cc_start: 0.8272 (mt0) cc_final: 0.8057 (tt0) REVERT: C 899 GLU cc_start: 0.7493 (pt0) cc_final: 0.7206 (pt0) REVERT: C 937 ASP cc_start: 0.6773 (m-30) cc_final: 0.6467 (m-30) REVERT: C 950 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7384 (tm-30) REVERT: C 955 GLN cc_start: 0.8276 (tp40) cc_final: 0.8041 (tp-100) REVERT: C 1131 MET cc_start: 0.8390 (mtt) cc_final: 0.8156 (mtt) REVERT: C 1171 ARG cc_start: 0.7497 (ttp80) cc_final: 0.7245 (ttp-110) REVERT: D 312 ARG cc_start: 0.7230 (ttp-170) cc_final: 0.6906 (tmt90) REVERT: D 1025 MET cc_start: 0.7718 (ttp) cc_final: 0.7336 (ttm) REVERT: D 1095 MET cc_start: 0.5853 (tmm) cc_final: 0.5595 (tpt) REVERT: D 1231 ARG cc_start: 0.7180 (ttp-110) cc_final: 0.6935 (ttm170) REVERT: D 1297 LYS cc_start: 0.7505 (mtpt) cc_final: 0.7198 (mtmt) REVERT: D 1334 GLU cc_start: 0.7505 (pt0) cc_final: 0.6931 (pp20) REVERT: E 67 ARG cc_start: 0.7536 (mtt90) cc_final: 0.7297 (mtt90) REVERT: F 160 ASP cc_start: 0.7981 (t0) cc_final: 0.7388 (p0) REVERT: F 277 MET cc_start: 0.7622 (tmm) cc_final: 0.6726 (tpt) REVERT: G 12 ARG cc_start: 0.7370 (mtt90) cc_final: 0.7159 (mtt90) REVERT: G 56 ARG cc_start: 0.7258 (ttp-170) cc_final: 0.6946 (ttm-80) REVERT: G 95 MET cc_start: 0.7195 (mtp) cc_final: 0.6934 (ttm) REVERT: G 231 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7519 (pp20) REVERT: H 39 ARG cc_start: 0.6931 (mtt90) cc_final: 0.6684 (mtt90) REVERT: H 60 PHE cc_start: 0.7739 (m-80) cc_final: 0.7458 (m-80) REVERT: H 112 MET cc_start: 0.4435 (tpt) cc_final: 0.3347 (mtm) REVERT: H 174 TYR cc_start: 0.5876 (t80) cc_final: 0.5494 (t80) outliers start: 0 outliers final: 1 residues processed: 494 average time/residue: 0.9280 time to fit residues: 529.6868 Evaluate side-chains 355 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 500 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 194 GLN B 66 HIS B 93 GLN B 132 HIS C 31 GLN C 36 GLN C 69 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 518 ASN C 620 ASN C 649 GLN C 725 GLN C 799 ASN C 856 ASN C1013 GLN C1237 HIS C1257 GLN C1268 GLN D 45 ASN D 157 GLN D 274 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN D 340 GLN D 341 ASN D 365 GLN D 424 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN D 962 ASN D1197 ASN D1244 GLN E 72 GLN F 131 GLN F 227 GLN F 309 ASN F 338 HIS ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 HIS F 579 GLN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 ASN G 51 GLN G 115 GLN G 154 ASN G 188 ASN ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 50 HIS ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.173586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105689 restraints weight = 38330.424| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.75 r_work: 0.3195 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36606 Z= 0.152 Angle : 0.620 9.691 49943 Z= 0.337 Chirality : 0.045 0.320 5681 Planarity : 0.005 0.059 6095 Dihedral : 16.177 178.139 5810 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.70 % Allowed : 12.21 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.23 (0.12), residues: 4194 helix: -0.29 (0.12), residues: 1662 sheet: -1.25 (0.20), residues: 501 loop : -1.05 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 220 TYR 0.017 0.001 TYR H 127 PHE 0.028 0.002 PHE H 7 TRP 0.015 0.001 TRP H 229 HIS 0.017 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (36598) covalent geometry : angle 0.61778 / 0.34 (49931) hydrogen bonds : bond 0.04488 / 3.07 ( 1632) hydrogen bonds : angle 5.22841 / 3.63 ( 4567) metal coordination : bond 0.00854 / 0.39 ( 8) metal coordination : angle 3.24097 / 1.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 392 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 THR cc_start: 0.8592 (t) cc_final: 0.8325 (m) REVERT: A 137 ASN cc_start: 0.8583 (m-40) cc_final: 0.8302 (m-40) REVERT: B 6 THR cc_start: 0.8502 (p) cc_final: 0.8072 (m) REVERT: B 18 GLN cc_start: 0.8499 (mt0) cc_final: 0.8013 (mm-40) REVERT: B 58 GLU cc_start: 0.8503 (pt0) cc_final: 0.8154 (pt0) REVERT: B 104 LYS cc_start: 0.7448 (tptm) cc_final: 0.7152 (tptp) REVERT: B 186 ASN cc_start: 0.8664 (t0) cc_final: 0.8401 (t0) REVERT: B 191 ARG cc_start: 0.7791 (ttp80) cc_final: 0.6859 (ptm-80) REVERT: C 118 LYS cc_start: 0.8129 (mttm) cc_final: 0.7529 (ttmt) REVERT: C 386 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7716 (tm-30) REVERT: C 439 LYS cc_start: 0.8142 (mttm) cc_final: 0.7791 (mtmt) REVERT: C 600 THR cc_start: 0.8780 (m) cc_final: 0.8517 (p) REVERT: C 738 GLU cc_start: 0.7784 (mp0) cc_final: 0.7570 (mm-30) REVERT: C 834 GLN cc_start: 0.8724 (mt0) cc_final: 0.8301 (tt0) REVERT: C 937 ASP cc_start: 0.7172 (m-30) cc_final: 0.6719 (m-30) REVERT: C 950 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7728 (tm-30) REVERT: C 955 GLN cc_start: 0.8265 (tp40) cc_final: 0.7982 (tp40) REVERT: C 1131 MET cc_start: 0.8343 (mtt) cc_final: 0.8124 (mtt) REVERT: C 1171 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7521 (ttp-110) REVERT: D 140 TYR cc_start: 0.7978 (m-10) cc_final: 0.7768 (m-10) REVERT: D 148 GLU cc_start: 0.8287 (pt0) cc_final: 0.7506 (tp30) REVERT: D 158 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: D 312 ARG cc_start: 0.7469 (ttp-170) cc_final: 0.6893 (tmt90) REVERT: D 388 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7650 (mtm180) REVERT: D 666 GLU cc_start: 0.7026 (pp20) cc_final: 0.6727 (pp20) REVERT: D 894 VAL cc_start: 0.8769 (t) cc_final: 0.8545 (m) REVERT: D 1095 MET cc_start: 0.6079 (tmm) cc_final: 0.5756 (tpp) REVERT: D 1231 ARG cc_start: 0.7430 (ttp-110) cc_final: 0.7104 (ttm170) REVERT: D 1334 GLU cc_start: 0.8189 (pt0) cc_final: 0.7904 (mt-10) REVERT: E 11 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7669 (tm-30) REVERT: E 79 GLU cc_start: 0.3398 (OUTLIER) cc_final: 0.3176 (pm20) REVERT: F 160 ASP cc_start: 0.8060 (t0) cc_final: 0.7350 (p0) REVERT: F 277 MET cc_start: 0.7352 (tmm) cc_final: 0.6838 (tpt) REVERT: G 12 ARG cc_start: 0.7755 (mtt90) cc_final: 0.7551 (mtt90) REVERT: G 56 ARG cc_start: 0.6973 (ttp-170) cc_final: 0.6610 (ttm-80) REVERT: G 95 MET cc_start: 0.6858 (mtp) cc_final: 0.6520 (ttm) REVERT: G 231 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7688 (pp20) REVERT: H 60 PHE cc_start: 0.7552 (m-80) cc_final: 0.7275 (m-80) REVERT: H 105 HIS cc_start: 0.5409 (OUTLIER) cc_final: 0.4016 (t70) REVERT: H 261 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7548 (tm-30) outliers start: 62 outliers final: 19 residues processed: 422 average time/residue: 0.8527 time to fit residues: 420.4837 Evaluate side-chains 359 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 336 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain H residue 105 HIS Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 56 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 351 optimal weight: 3.9990 chunk 312 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 391 optimal weight: 8.9990 chunk 385 optimal weight: 10.0000 chunk 362 optimal weight: 3.9990 chunk 352 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 227 GLN C 41 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS D 340 GLN D 364 HIS D 488 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN D1197 ASN D1366 HIS F 128 ASN F 406 GLN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.170600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.101439 restraints weight = 37921.778| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.76 r_work: 0.3138 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 36606 Z= 0.276 Angle : 0.654 12.543 49943 Z= 0.351 Chirality : 0.048 0.337 5681 Planarity : 0.005 0.065 6095 Dihedral : 16.137 176.375 5810 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.30 % Allowed : 14.10 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.82 (0.12), residues: 4194 helix: 0.12 (0.12), residues: 1666 sheet: -1.14 (0.20), residues: 560 loop : -0.83 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 352 TYR 0.016 0.002 TYR D 631 PHE 0.038 0.002 PHE H 7 TRP 0.011 0.001 TRP H 229 HIS 0.015 0.002 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.28 (36598) covalent geometry : angle 0.65203 / 0.35 (49931) hydrogen bonds : bond 0.04821 / 3.31 ( 1632) hydrogen bonds : angle 5.05336 / 3.52 ( 4567) metal coordination : bond 0.01202 / 0.57 ( 8) metal coordination : angle 3.37594 / 1.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 354 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 THR cc_start: 0.8623 (t) cc_final: 0.8390 (m) REVERT: B 6 THR cc_start: 0.8512 (p) cc_final: 0.8077 (m) REVERT: B 18 GLN cc_start: 0.8541 (mt0) cc_final: 0.8017 (mm-40) REVERT: B 58 GLU cc_start: 0.8597 (pt0) cc_final: 0.8185 (pt0) REVERT: B 104 LYS cc_start: 0.7415 (tptm) cc_final: 0.7121 (tptp) REVERT: B 191 ARG cc_start: 0.7865 (ttp80) cc_final: 0.6570 (ttp80) REVERT: C 118 LYS cc_start: 0.8110 (mttm) cc_final: 0.7412 (ttmm) REVERT: C 386 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 439 LYS cc_start: 0.8240 (mttm) cc_final: 0.7878 (mtmt) REVERT: C 515 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.7513 (tmm) REVERT: C 600 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8617 (p) REVERT: C 834 GLN cc_start: 0.8761 (mt0) cc_final: 0.8355 (tt0) REVERT: C 937 ASP cc_start: 0.7296 (m-30) cc_final: 0.6907 (m-30) REVERT: C 950 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7678 (tm-30) REVERT: C 955 GLN cc_start: 0.8252 (tp40) cc_final: 0.7931 (tp40) REVERT: C 1131 MET cc_start: 0.8423 (mtt) cc_final: 0.8196 (mtt) REVERT: C 1171 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7501 (ttp-110) REVERT: D 140 TYR cc_start: 0.8073 (m-10) cc_final: 0.7840 (m-10) REVERT: D 148 GLU cc_start: 0.8330 (pt0) cc_final: 0.7516 (tp30) REVERT: D 158 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: D 312 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.6934 (tmt90) REVERT: D 388 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7768 (mtm180) REVERT: D 666 GLU cc_start: 0.7125 (pp20) cc_final: 0.6832 (pp20) REVERT: D 707 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7758 (tp) REVERT: D 1095 MET cc_start: 0.6288 (tmm) cc_final: 0.5900 (tpt) REVERT: D 1231 ARG cc_start: 0.7471 (ttp-110) cc_final: 0.7146 (ttm170) REVERT: E 11 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7739 (tm-30) REVERT: E 56 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8238 (mt-10) REVERT: E 79 GLU cc_start: 0.3044 (OUTLIER) cc_final: 0.2835 (pm20) REVERT: F 160 ASP cc_start: 0.8050 (t0) cc_final: 0.7344 (p0) REVERT: F 277 MET cc_start: 0.7332 (tmm) cc_final: 0.6775 (tmm) REVERT: F 367 ILE cc_start: 0.7959 (mt) cc_final: 0.7735 (mp) REVERT: F 474 MET cc_start: 0.8121 (mtp) cc_final: 0.7915 (mtp) REVERT: G 56 ARG cc_start: 0.7030 (ttp-170) cc_final: 0.6686 (ttm-80) REVERT: G 95 MET cc_start: 0.6861 (mtp) cc_final: 0.6600 (ttm) REVERT: G 231 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7753 (pp20) REVERT: H 47 MET cc_start: 0.7284 (tpp) cc_final: 0.6991 (tpp) REVERT: H 60 PHE cc_start: 0.7593 (m-80) cc_final: 0.7304 (m-80) REVERT: H 259 MET cc_start: 0.7716 (ttp) cc_final: 0.7330 (ptm) REVERT: H 261 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7493 (tm-30) outliers start: 84 outliers final: 33 residues processed: 400 average time/residue: 0.8385 time to fit residues: 391.2392 Evaluate side-chains 373 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 334 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 161 optimal weight: 0.0970 chunk 130 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 271 optimal weight: 20.0000 chunk 331 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN D 979 ASN D1197 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 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 = 0.4145 r_free = 0.4145 target = 0.172928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.104573 restraints weight = 37765.116| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.74 r_work: 0.3187 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36606 Z= 0.147 Angle : 0.559 13.308 49943 Z= 0.303 Chirality : 0.044 0.328 5681 Planarity : 0.004 0.061 6095 Dihedral : 16.049 177.512 5808 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.00 % Allowed : 15.42 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.12), residues: 4194 helix: 0.59 (0.13), residues: 1664 sheet: -0.93 (0.21), residues: 509 loop : -0.67 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 281 TYR 0.016 0.001 TYR D 631 PHE 0.041 0.001 PHE H 7 TRP 0.011 0.001 TRP H 229 HIS 0.021 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (36598) covalent geometry : angle 0.55749 / 0.30 (49931) hydrogen bonds : bond 0.03988 / 2.72 ( 1632) hydrogen bonds : angle 4.78377 / 3.32 ( 4567) metal coordination : bond 0.00393 / 0.20 ( 8) metal coordination : angle 2.42764 / 1.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 359 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: A 116 THR cc_start: 0.8584 (t) cc_final: 0.8368 (m) REVERT: A 137 ASN cc_start: 0.8524 (m-40) cc_final: 0.8260 (m-40) REVERT: A 199 ASP cc_start: 0.8036 (m-30) cc_final: 0.7786 (m-30) REVERT: B 6 THR cc_start: 0.8521 (p) cc_final: 0.8097 (m) REVERT: B 18 GLN cc_start: 0.8523 (mt0) cc_final: 0.8038 (mm-40) REVERT: B 58 GLU cc_start: 0.8575 (pt0) cc_final: 0.8153 (pt0) REVERT: B 104 LYS cc_start: 0.7429 (tptm) cc_final: 0.7137 (tptp) REVERT: B 186 ASN cc_start: 0.8550 (t0) cc_final: 0.8303 (t0) REVERT: B 188 GLU cc_start: 0.8760 (pm20) cc_final: 0.8464 (mp0) REVERT: B 191 ARG cc_start: 0.7750 (ttp80) cc_final: 0.6530 (ttp80) REVERT: C 118 LYS cc_start: 0.8122 (mttm) cc_final: 0.7704 (ttmm) REVERT: C 386 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 439 LYS cc_start: 0.8188 (mttm) cc_final: 0.7848 (mtmt) REVERT: C 515 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7452 (tmm) REVERT: C 739 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7879 (p0) REVERT: C 779 ARG cc_start: 0.8564 (ttt90) cc_final: 0.8146 (ttt-90) REVERT: C 834 GLN cc_start: 0.8746 (mt0) cc_final: 0.8336 (tt0) REVERT: C 937 ASP cc_start: 0.7321 (m-30) cc_final: 0.6875 (m-30) REVERT: C 955 GLN cc_start: 0.8284 (tp40) cc_final: 0.7994 (tp40) REVERT: C 1171 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7491 (ttp-110) REVERT: D 148 GLU cc_start: 0.8442 (pt0) cc_final: 0.7591 (tp30) REVERT: D 158 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: D 289 ASP cc_start: 0.7861 (t70) cc_final: 0.7548 (m-30) REVERT: D 312 ARG cc_start: 0.7574 (ttp-170) cc_final: 0.6946 (tmt90) REVERT: D 330 MET cc_start: 0.8549 (mmt) cc_final: 0.8278 (mmt) REVERT: D 388 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7749 (mtm180) REVERT: D 666 GLU cc_start: 0.7174 (pp20) cc_final: 0.6886 (pp20) REVERT: D 707 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7599 (tp) REVERT: D 1095 MET cc_start: 0.6156 (tmm) cc_final: 0.5788 (tpt) REVERT: D 1231 ARG cc_start: 0.7457 (ttp-110) cc_final: 0.7173 (ttm170) REVERT: E 11 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7576 (mt-10) REVERT: E 56 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8236 (mt-10) REVERT: F 160 ASP cc_start: 0.8021 (t0) cc_final: 0.7393 (p0) REVERT: F 277 MET cc_start: 0.7424 (tmm) cc_final: 0.6684 (tmm) REVERT: F 354 THR cc_start: 0.7627 (OUTLIER) cc_final: 0.7209 (p) REVERT: G 12 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7555 (mtt180) REVERT: G 56 ARG cc_start: 0.7025 (ttp-170) cc_final: 0.6669 (ttm-80) REVERT: G 95 MET cc_start: 0.6778 (mtp) cc_final: 0.6494 (ttm) REVERT: G 112 MET cc_start: 0.4340 (mpp) cc_final: 0.4140 (mmp) REVERT: G 231 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7779 (pp20) REVERT: H 60 PHE cc_start: 0.7562 (m-80) cc_final: 0.7270 (m-80) REVERT: H 261 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7506 (tm-30) outliers start: 73 outliers final: 33 residues processed: 399 average time/residue: 0.8445 time to fit residues: 393.8749 Evaluate side-chains 364 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 324 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 365 optimal weight: 1.9990 chunk 233 optimal weight: 0.0870 chunk 30 optimal weight: 0.0000 chunk 268 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 199 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 398 optimal weight: 9.9990 overall best weight: 0.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1244 HIS D 320 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN D1197 ASN F 342 GLN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.174045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106064 restraints weight = 37849.326| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.75 r_work: 0.3204 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36606 Z= 0.127 Angle : 0.530 13.337 49943 Z= 0.287 Chirality : 0.043 0.324 5681 Planarity : 0.004 0.060 6095 Dihedral : 15.888 177.986 5808 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.09 % Allowed : 16.24 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.05 (0.13), residues: 4194 helix: 0.90 (0.13), residues: 1677 sheet: -0.81 (0.21), residues: 506 loop : -0.55 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 143 TYR 0.015 0.001 TYR D 631 PHE 0.041 0.001 PHE H 7 TRP 0.010 0.001 TRP H 229 HIS 0.019 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (36598) covalent geometry : angle 0.52841 / 0.29 (49931) hydrogen bonds : bond 0.03728 / 2.54 ( 1632) hydrogen bonds : angle 4.55498 / 3.17 ( 4567) metal coordination : bond 0.00404 / 0.22 ( 8) metal coordination : angle 2.48613 / 1.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 360 time to evaluate : 1.274 Fit side-chains REVERT: A 116 THR cc_start: 0.8549 (t) cc_final: 0.8318 (m) REVERT: A 137 ASN cc_start: 0.8465 (m-40) cc_final: 0.8220 (m-40) REVERT: A 199 ASP cc_start: 0.7933 (m-30) cc_final: 0.7667 (m-30) REVERT: A 200 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8209 (ptpp) REVERT: B 6 THR cc_start: 0.8516 (p) cc_final: 0.8119 (m) REVERT: B 18 GLN cc_start: 0.8459 (mt0) cc_final: 0.7975 (mm-40) REVERT: B 58 GLU cc_start: 0.8546 (pt0) cc_final: 0.8122 (pt0) REVERT: B 104 LYS cc_start: 0.7349 (tptm) cc_final: 0.7041 (tptp) REVERT: B 186 ASN cc_start: 0.8548 (t0) cc_final: 0.8318 (t0) REVERT: B 188 GLU cc_start: 0.8777 (pm20) cc_final: 0.8464 (mp0) REVERT: C 90 VAL cc_start: 0.8793 (p) cc_final: 0.8535 (m) REVERT: C 118 LYS cc_start: 0.8101 (mttm) cc_final: 0.7898 (tppt) REVERT: C 239 MET cc_start: 0.5670 (OUTLIER) cc_final: 0.5210 (tmm) REVERT: C 386 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 439 LYS cc_start: 0.8214 (mttm) cc_final: 0.7873 (mtmt) REVERT: C 515 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7471 (tmm) REVERT: C 739 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7984 (p0) REVERT: C 779 ARG cc_start: 0.8535 (ttt90) cc_final: 0.8142 (ttt-90) REVERT: C 834 GLN cc_start: 0.8732 (mt0) cc_final: 0.8329 (tt0) REVERT: C 937 ASP cc_start: 0.7312 (m-30) cc_final: 0.6864 (m-30) REVERT: C 955 GLN cc_start: 0.8227 (tp40) cc_final: 0.7895 (tp40) REVERT: C 1171 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7491 (ttp-110) REVERT: D 148 GLU cc_start: 0.8518 (pt0) cc_final: 0.8034 (pp20) REVERT: D 158 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: D 289 ASP cc_start: 0.7925 (t70) cc_final: 0.7407 (m-30) REVERT: D 293 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7748 (mtm180) REVERT: D 312 ARG cc_start: 0.7550 (ttp-170) cc_final: 0.6899 (tmt90) REVERT: D 516 ASP cc_start: 0.8301 (p0) cc_final: 0.8051 (p0) REVERT: D 666 GLU cc_start: 0.7159 (pp20) cc_final: 0.6913 (pp20) REVERT: D 707 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7559 (tp) REVERT: D 1095 MET cc_start: 0.6261 (tmm) cc_final: 0.5877 (tpt) REVERT: D 1231 ARG cc_start: 0.7437 (ttp-110) cc_final: 0.7129 (ttm170) REVERT: E 11 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7525 (mt-10) REVERT: E 56 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8224 (mt-10) REVERT: E 67 ARG cc_start: 0.7329 (mtt90) cc_final: 0.7052 (mtt90) REVERT: F 160 ASP cc_start: 0.8039 (t0) cc_final: 0.7481 (p0) REVERT: F 277 MET cc_start: 0.7399 (tmm) cc_final: 0.6667 (tmm) REVERT: F 354 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7259 (p) REVERT: G 12 ARG cc_start: 0.7811 (mpp80) cc_final: 0.7570 (mtt180) REVERT: G 56 ARG cc_start: 0.7033 (ttp-170) cc_final: 0.6685 (ttm-80) REVERT: G 95 MET cc_start: 0.6780 (mtp) cc_final: 0.6495 (ttm) REVERT: G 231 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7775 (pp20) REVERT: H 60 PHE cc_start: 0.7564 (m-80) cc_final: 0.7226 (m-80) REVERT: H 231 GLU cc_start: 0.7675 (mm-30) cc_final: 0.6827 (pp20) REVERT: H 261 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7257 (tm-30) outliers start: 76 outliers final: 34 residues processed: 405 average time/residue: 0.8234 time to fit residues: 391.6869 Evaluate side-chains 377 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 336 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 313 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 420 optimal weight: 8.9990 chunk 70 optimal weight: 0.0670 chunk 299 optimal weight: 4.9990 chunk 49 optimal weight: 0.0270 chunk 380 optimal weight: 0.9990 chunk 62 optimal weight: 0.0970 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1244 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D1197 ASN F 446 GLN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 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 = 0.4171 r_free = 0.4171 target = 0.175364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107804 restraints weight = 37967.211| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.75 r_work: 0.3233 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36606 Z= 0.107 Angle : 0.514 12.769 49943 Z= 0.279 Chirality : 0.042 0.321 5681 Planarity : 0.004 0.059 6095 Dihedral : 15.760 178.560 5808 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.65 % Allowed : 17.53 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4194 helix: 1.09 (0.13), residues: 1685 sheet: -0.71 (0.21), residues: 505 loop : -0.41 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 903 TYR 0.014 0.001 TYR D 631 PHE 0.043 0.001 PHE H 7 TRP 0.010 0.001 TRP D1193 HIS 0.012 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 (36598) covalent geometry : angle 0.51311 / 0.28 (49931) hydrogen bonds : bond 0.03478 / 2.37 ( 1632) hydrogen bonds : angle 4.42313 / 3.07 ( 4567) metal coordination : bond 0.00311 / 0.17 ( 8) metal coordination : angle 2.18101 / 1.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 362 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: A 116 THR cc_start: 0.8460 (t) cc_final: 0.8233 (m) REVERT: A 137 ASN cc_start: 0.8396 (m-40) cc_final: 0.8131 (m-40) REVERT: A 199 ASP cc_start: 0.7782 (m-30) cc_final: 0.7519 (m-30) REVERT: B 6 THR cc_start: 0.8479 (p) cc_final: 0.8102 (m) REVERT: B 18 GLN cc_start: 0.8448 (mt0) cc_final: 0.7983 (mm-40) REVERT: B 51 MET cc_start: 0.9137 (mmm) cc_final: 0.8835 (tpt) REVERT: B 58 GLU cc_start: 0.8546 (pt0) cc_final: 0.8113 (pt0) REVERT: B 104 LYS cc_start: 0.7270 (tptm) cc_final: 0.6954 (tptp) REVERT: B 186 ASN cc_start: 0.8526 (t0) cc_final: 0.8226 (t0) REVERT: B 188 GLU cc_start: 0.8773 (pm20) cc_final: 0.8455 (mp0) REVERT: C 20 GLN cc_start: 0.8191 (mt0) cc_final: 0.7608 (tm-30) REVERT: C 90 VAL cc_start: 0.8733 (p) cc_final: 0.8467 (m) REVERT: C 239 MET cc_start: 0.5619 (OUTLIER) cc_final: 0.5139 (tmm) REVERT: C 386 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7502 (tm-30) REVERT: C 439 LYS cc_start: 0.8290 (mttm) cc_final: 0.7939 (mtmt) REVERT: C 515 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7363 (tmm) REVERT: C 779 ARG cc_start: 0.8474 (ttt90) cc_final: 0.8009 (ttt-90) REVERT: C 834 GLN cc_start: 0.8702 (mt0) cc_final: 0.8269 (tt0) REVERT: C 937 ASP cc_start: 0.7210 (m-30) cc_final: 0.6746 (m-30) REVERT: C 949 GLU cc_start: 0.8254 (tt0) cc_final: 0.7496 (tt0) REVERT: C 955 GLN cc_start: 0.8160 (tp40) cc_final: 0.7814 (tp40) REVERT: C 1024 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6576 (mm-30) REVERT: C 1171 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7504 (ttp-110) REVERT: D 140 TYR cc_start: 0.7944 (m-10) cc_final: 0.7737 (m-10) REVERT: D 148 GLU cc_start: 0.8515 (pt0) cc_final: 0.8017 (pp20) REVERT: D 158 GLN cc_start: 0.8891 (tt0) cc_final: 0.8431 (tt0) REVERT: D 162 GLU cc_start: 0.8356 (tp30) cc_final: 0.8091 (tm-30) REVERT: D 289 ASP cc_start: 0.7856 (t70) cc_final: 0.7317 (m-30) REVERT: D 293 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7713 (mtm180) REVERT: D 312 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.6798 (tmt90) REVERT: D 516 ASP cc_start: 0.8303 (p0) cc_final: 0.8030 (p0) REVERT: D 707 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7419 (tt) REVERT: D 932 MET cc_start: 0.7705 (ttt) cc_final: 0.7475 (ttm) REVERT: D 1040 MET cc_start: 0.2798 (ptt) cc_final: 0.2420 (pmt) REVERT: D 1095 MET cc_start: 0.6255 (tmm) cc_final: 0.5863 (tpt) REVERT: D 1231 ARG cc_start: 0.7375 (ttp-110) cc_final: 0.7040 (ttm170) REVERT: E 11 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7442 (mt-10) REVERT: E 56 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8120 (mt-10) REVERT: E 67 ARG cc_start: 0.7263 (mtt90) cc_final: 0.6974 (mtt90) REVERT: F 160 ASP cc_start: 0.8037 (t0) cc_final: 0.7470 (p0) REVERT: F 277 MET cc_start: 0.7379 (tmm) cc_final: 0.6646 (tmm) REVERT: F 354 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7310 (p) REVERT: G 56 ARG cc_start: 0.6992 (ttp-170) cc_final: 0.6626 (ttm-80) REVERT: G 95 MET cc_start: 0.6712 (mtp) cc_final: 0.6484 (ttm) REVERT: G 231 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7787 (pp20) REVERT: H 60 PHE cc_start: 0.7492 (m-80) cc_final: 0.7122 (m-80) REVERT: H 231 GLU cc_start: 0.7704 (mm-30) cc_final: 0.6832 (pp20) outliers start: 60 outliers final: 25 residues processed: 397 average time/residue: 0.8356 time to fit residues: 389.5651 Evaluate side-chains 358 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 328 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 206 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 63 optimal weight: 5.9990 chunk 300 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 280 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 369 optimal weight: 10.9990 chunk 33 optimal weight: 9.9990 chunk 315 optimal weight: 2.9990 chunk 405 optimal weight: 9.9990 chunk 189 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 ASN C1244 HIS D1197 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.171646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102768 restraints weight = 38004.233| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.75 r_work: 0.3156 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 36606 Z= 0.232 Angle : 0.600 14.391 49943 Z= 0.318 Chirality : 0.046 0.332 5681 Planarity : 0.004 0.062 6095 Dihedral : 15.858 177.021 5808 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.14 % Allowed : 17.89 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.05 (0.13), residues: 4194 helix: 0.90 (0.13), residues: 1688 sheet: -0.65 (0.21), residues: 515 loop : -0.43 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 97 TYR 0.016 0.002 TYR D 631 PHE 0.045 0.002 PHE H 7 TRP 0.008 0.001 TRP D1193 HIS 0.012 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (36598) covalent geometry : angle 0.59832 / 0.32 (49931) hydrogen bonds : bond 0.04196 / 2.88 ( 1632) hydrogen bonds : angle 4.57207 / 3.18 ( 4567) metal coordination : bond 0.00798 / 0.38 ( 8) metal coordination : angle 2.77141 / 1.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 336 time to evaluate : 1.394 Fit side-chains REVERT: A 116 THR cc_start: 0.8501 (t) cc_final: 0.8290 (m) REVERT: A 137 ASN cc_start: 0.8477 (m-40) cc_final: 0.8224 (m-40) REVERT: A 199 ASP cc_start: 0.7898 (m-30) cc_final: 0.7628 (m-30) REVERT: B 6 THR cc_start: 0.8511 (p) cc_final: 0.8097 (m) REVERT: B 18 GLN cc_start: 0.8525 (mt0) cc_final: 0.8033 (mm-40) REVERT: B 58 GLU cc_start: 0.8662 (pt0) cc_final: 0.8260 (pt0) REVERT: B 104 LYS cc_start: 0.7316 (tptm) cc_final: 0.6983 (tptp) REVERT: B 188 GLU cc_start: 0.8736 (pm20) cc_final: 0.8458 (mp0) REVERT: B 205 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8424 (ttt) REVERT: C 90 VAL cc_start: 0.8830 (p) cc_final: 0.8570 (m) REVERT: C 239 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5166 (tmm) REVERT: C 386 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7663 (tm-30) REVERT: C 439 LYS cc_start: 0.8229 (mttm) cc_final: 0.7879 (mtmt) REVERT: C 515 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.7593 (tmm) REVERT: C 779 ARG cc_start: 0.8621 (ttt90) cc_final: 0.8220 (ttt-90) REVERT: C 834 GLN cc_start: 0.8731 (mt0) cc_final: 0.8343 (tt0) REVERT: C 955 GLN cc_start: 0.8250 (tp40) cc_final: 0.7948 (tp40) REVERT: C 1171 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7529 (ttp-110) REVERT: C 1219 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8302 (pt0) REVERT: D 140 TYR cc_start: 0.8064 (m-10) cc_final: 0.7839 (m-10) REVERT: D 148 GLU cc_start: 0.8538 (pt0) cc_final: 0.8051 (pp20) REVERT: D 158 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: D 162 GLU cc_start: 0.8439 (tp30) cc_final: 0.8169 (tm-30) REVERT: D 312 ARG cc_start: 0.7570 (ttp-170) cc_final: 0.6917 (tmt90) REVERT: D 388 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7871 (mtm180) REVERT: D 516 ASP cc_start: 0.8345 (p0) cc_final: 0.8128 (p0) REVERT: D 666 GLU cc_start: 0.7041 (pp20) cc_final: 0.6740 (pp20) REVERT: D 707 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7683 (tp) REVERT: D 901 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8422 (ttm170) REVERT: D 1040 MET cc_start: 0.2072 (ptt) cc_final: 0.1785 (pmt) REVERT: D 1095 MET cc_start: 0.6199 (tmm) cc_final: 0.5822 (tpp) REVERT: D 1231 ARG cc_start: 0.7482 (ttp-110) cc_final: 0.7174 (ttm170) REVERT: D 1327 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: E 11 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7588 (mt-10) REVERT: E 56 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8225 (mt-10) REVERT: F 160 ASP cc_start: 0.8026 (t0) cc_final: 0.7506 (p0) REVERT: F 277 MET cc_start: 0.7408 (tmm) cc_final: 0.6703 (tmm) REVERT: F 354 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7322 (p) REVERT: G 12 ARG cc_start: 0.7768 (mpp80) cc_final: 0.7557 (mtt180) REVERT: G 56 ARG cc_start: 0.6992 (ttp-170) cc_final: 0.6664 (ttm-80) REVERT: G 95 MET cc_start: 0.6831 (mtp) cc_final: 0.6475 (ttm) REVERT: G 231 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7815 (pp20) REVERT: H 60 PHE cc_start: 0.7599 (m-80) cc_final: 0.7245 (m-80) REVERT: H 231 GLU cc_start: 0.7760 (mm-30) cc_final: 0.6854 (pp20) outliers start: 78 outliers final: 42 residues processed: 386 average time/residue: 0.8420 time to fit residues: 380.3780 Evaluate side-chains 378 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 326 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain F residue 604 SER Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 302 optimal weight: 2.9990 chunk 426 optimal weight: 8.9990 chunk 291 optimal weight: 8.9990 chunk 258 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 214 optimal weight: 0.6980 chunk 358 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C1244 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.174329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.106411 restraints weight = 38114.053| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.75 r_work: 0.3215 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36606 Z= 0.119 Angle : 0.528 14.270 49943 Z= 0.283 Chirality : 0.042 0.323 5681 Planarity : 0.004 0.060 6095 Dihedral : 15.790 178.509 5808 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.29 % Allowed : 18.93 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.25 (0.13), residues: 4194 helix: 1.09 (0.13), residues: 1693 sheet: -0.55 (0.22), residues: 486 loop : -0.36 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 77 TYR 0.018 0.001 TYR H 102 PHE 0.052 0.001 PHE H 7 TRP 0.033 0.001 TRP D1193 HIS 0.012 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (36598) covalent geometry : angle 0.52678 / 0.28 (49931) hydrogen bonds : bond 0.03548 / 2.42 ( 1632) hydrogen bonds : angle 4.40665 / 3.06 ( 4567) metal coordination : bond 0.00400 / 0.22 ( 8) metal coordination : angle 1.94400 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 348 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 116 THR cc_start: 0.8459 (t) cc_final: 0.8240 (m) REVERT: A 137 ASN cc_start: 0.8450 (m-40) cc_final: 0.8192 (m-40) REVERT: A 199 ASP cc_start: 0.7802 (m-30) cc_final: 0.7587 (m-30) REVERT: B 6 THR cc_start: 0.8502 (p) cc_final: 0.8099 (m) REVERT: B 18 GLN cc_start: 0.8472 (mt0) cc_final: 0.8011 (mm-40) REVERT: B 51 MET cc_start: 0.9143 (mmm) cc_final: 0.8845 (tpt) REVERT: B 58 GLU cc_start: 0.8613 (pt0) cc_final: 0.8193 (pt0) REVERT: B 104 LYS cc_start: 0.7260 (tptm) cc_final: 0.6927 (tptp) REVERT: B 186 ASN cc_start: 0.8468 (t0) cc_final: 0.8253 (t0) REVERT: B 188 GLU cc_start: 0.8725 (pm20) cc_final: 0.8508 (mp0) REVERT: C 20 GLN cc_start: 0.8177 (mt0) cc_final: 0.7620 (tm-30) REVERT: C 90 VAL cc_start: 0.8757 (p) cc_final: 0.8504 (m) REVERT: C 239 MET cc_start: 0.5685 (OUTLIER) cc_final: 0.5222 (tmm) REVERT: C 386 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7569 (tm-30) REVERT: C 439 LYS cc_start: 0.8144 (mttm) cc_final: 0.7873 (mtpt) REVERT: C 515 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7408 (tmm) REVERT: C 540 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7974 (ttp-170) REVERT: C 834 GLN cc_start: 0.8696 (mt0) cc_final: 0.8265 (tt0) REVERT: C 943 LYS cc_start: 0.8420 (mtpp) cc_final: 0.7939 (ptmm) REVERT: C 949 GLU cc_start: 0.8298 (tt0) cc_final: 0.7466 (tt0) REVERT: C 955 GLN cc_start: 0.8185 (tp40) cc_final: 0.7830 (tp40) REVERT: C 1171 ARG cc_start: 0.7820 (ttp80) cc_final: 0.7541 (ttp-110) REVERT: D 140 TYR cc_start: 0.7955 (m-10) cc_final: 0.7752 (m-10) REVERT: D 148 GLU cc_start: 0.8518 (pt0) cc_final: 0.8027 (pp20) REVERT: D 158 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: D 162 GLU cc_start: 0.8397 (tp30) cc_final: 0.8134 (tm-30) REVERT: D 192 MET cc_start: 0.7791 (ptm) cc_final: 0.7529 (ptm) REVERT: D 293 ARG cc_start: 0.8098 (mtt180) cc_final: 0.7686 (mtm180) REVERT: D 312 ARG cc_start: 0.7504 (ttp-170) cc_final: 0.6841 (tmt90) REVERT: D 516 ASP cc_start: 0.8281 (p0) cc_final: 0.8068 (p0) REVERT: D 666 GLU cc_start: 0.7006 (pp20) cc_final: 0.6709 (pp20) REVERT: D 707 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7487 (tt) REVERT: D 901 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8451 (ttm170) REVERT: D 1040 MET cc_start: 0.2313 (ptt) cc_final: 0.1969 (pmt) REVERT: D 1095 MET cc_start: 0.6285 (tmm) cc_final: 0.5871 (tpp) REVERT: D 1231 ARG cc_start: 0.7426 (ttp-110) cc_final: 0.7173 (ttm170) REVERT: D 1327 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: E 11 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7500 (mt-10) REVERT: E 56 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8107 (mt-10) REVERT: E 67 ARG cc_start: 0.7289 (mtt90) cc_final: 0.7000 (mtt90) REVERT: F 160 ASP cc_start: 0.8003 (t0) cc_final: 0.7460 (p0) REVERT: F 277 MET cc_start: 0.7439 (tmm) cc_final: 0.7128 (tpt) REVERT: F 354 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7378 (p) REVERT: F 581 ASP cc_start: 0.7842 (t0) cc_final: 0.7364 (m-30) REVERT: F 604 SER cc_start: 0.7633 (OUTLIER) cc_final: 0.6789 (m) REVERT: G 12 ARG cc_start: 0.7757 (mpp80) cc_final: 0.7510 (mtt180) REVERT: G 56 ARG cc_start: 0.6981 (ttp-170) cc_final: 0.6651 (ttm-80) REVERT: G 95 MET cc_start: 0.6782 (mtp) cc_final: 0.6469 (ttm) REVERT: G 179 MET cc_start: 0.3437 (mpm) cc_final: 0.3210 (mtm) REVERT: G 231 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7791 (pp20) REVERT: H 60 PHE cc_start: 0.7524 (m-80) cc_final: 0.7149 (m-80) REVERT: H 231 GLU cc_start: 0.7750 (mm-30) cc_final: 0.6857 (pp20) outliers start: 47 outliers final: 25 residues processed: 378 average time/residue: 0.8609 time to fit residues: 380.9921 Evaluate side-chains 368 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 335 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 604 SER Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 381 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 289 optimal weight: 0.9980 chunk 294 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 266 optimal weight: 0.6980 chunk 112 optimal weight: 0.0670 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C1244 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.174463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107075 restraints weight = 38419.394| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.03 r_work: 0.3200 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36606 Z= 0.119 Angle : 0.522 13.650 49943 Z= 0.280 Chirality : 0.042 0.321 5681 Planarity : 0.004 0.060 6095 Dihedral : 15.685 178.459 5808 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.37 % Allowed : 19.04 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.13), residues: 4194 helix: 1.19 (0.13), residues: 1691 sheet: -0.59 (0.22), residues: 488 loop : -0.28 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 77 TYR 0.015 0.001 TYR H 102 PHE 0.043 0.001 PHE H 7 TRP 0.017 0.001 TRP D1193 HIS 0.010 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (36598) covalent geometry : angle 0.52089 / 0.28 (49931) hydrogen bonds : bond 0.03500 / 2.40 ( 1632) hydrogen bonds : angle 4.33716 / 3.01 ( 4567) metal coordination : bond 0.00372 / 0.20 ( 8) metal coordination : angle 2.05332 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 348 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 THR cc_start: 0.8444 (t) cc_final: 0.8231 (m) REVERT: A 137 ASN cc_start: 0.8413 (m-40) cc_final: 0.8172 (m-40) REVERT: A 214 GLU cc_start: 0.8125 (tt0) cc_final: 0.7901 (tt0) REVERT: B 6 THR cc_start: 0.8448 (p) cc_final: 0.8055 (m) REVERT: B 18 GLN cc_start: 0.8473 (mt0) cc_final: 0.8016 (mm-40) REVERT: B 51 MET cc_start: 0.9166 (mmm) cc_final: 0.8873 (tpt) REVERT: B 58 GLU cc_start: 0.8625 (pt0) cc_final: 0.8213 (pt0) REVERT: B 104 LYS cc_start: 0.7272 (tptm) cc_final: 0.6934 (tptp) REVERT: B 188 GLU cc_start: 0.8768 (pm20) cc_final: 0.8488 (mp0) REVERT: C 20 GLN cc_start: 0.8188 (mt0) cc_final: 0.7629 (tm-30) REVERT: C 90 VAL cc_start: 0.8787 (p) cc_final: 0.8533 (m) REVERT: C 239 MET cc_start: 0.5718 (OUTLIER) cc_final: 0.5266 (tmm) REVERT: C 386 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7539 (tm-30) REVERT: C 439 LYS cc_start: 0.8299 (mttm) cc_final: 0.8026 (mtpt) REVERT: C 515 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7428 (tmm) REVERT: C 540 ARG cc_start: 0.8214 (ttp-110) cc_final: 0.7954 (ttp-170) REVERT: C 641 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7801 (pt0) REVERT: C 779 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8075 (ttt-90) REVERT: C 834 GLN cc_start: 0.8726 (mt0) cc_final: 0.8314 (tt0) REVERT: C 943 LYS cc_start: 0.8431 (mtpp) cc_final: 0.7953 (ptmm) REVERT: C 949 GLU cc_start: 0.8318 (tt0) cc_final: 0.7495 (tt0) REVERT: C 955 GLN cc_start: 0.8206 (tp40) cc_final: 0.7860 (tp40) REVERT: C 1171 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7575 (ttp-110) REVERT: D 140 TYR cc_start: 0.7997 (m-10) cc_final: 0.7785 (m-10) REVERT: D 148 GLU cc_start: 0.8599 (pt0) cc_final: 0.8122 (pp20) REVERT: D 158 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: D 162 GLU cc_start: 0.8409 (tp30) cc_final: 0.8135 (tm-30) REVERT: D 192 MET cc_start: 0.7809 (ptm) cc_final: 0.7512 (ptm) REVERT: D 293 ARG cc_start: 0.8071 (mtt180) cc_final: 0.7640 (mtm180) REVERT: D 312 ARG cc_start: 0.7505 (ttp-170) cc_final: 0.6813 (tmt90) REVERT: D 516 ASP cc_start: 0.8325 (p0) cc_final: 0.8121 (p0) REVERT: D 666 GLU cc_start: 0.6990 (pp20) cc_final: 0.6718 (pp20) REVERT: D 901 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8450 (ttm170) REVERT: D 1040 MET cc_start: 0.2352 (ptt) cc_final: 0.1972 (pmt) REVERT: D 1095 MET cc_start: 0.6291 (tmm) cc_final: 0.5902 (tpp) REVERT: D 1231 ARG cc_start: 0.7515 (ttp-110) cc_final: 0.7178 (ttm170) REVERT: D 1327 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: E 11 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7501 (mt-10) REVERT: E 56 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8130 (mt-10) REVERT: F 160 ASP cc_start: 0.8004 (t0) cc_final: 0.7479 (p0) REVERT: F 273 MET cc_start: 0.7207 (tpt) cc_final: 0.6281 (tpt) REVERT: F 277 MET cc_start: 0.7497 (tmm) cc_final: 0.6957 (mmm) REVERT: F 354 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7557 (p) REVERT: F 581 ASP cc_start: 0.7850 (t0) cc_final: 0.7394 (m-30) REVERT: F 604 SER cc_start: 0.7693 (OUTLIER) cc_final: 0.6832 (m) REVERT: G 56 ARG cc_start: 0.6947 (ttp-170) cc_final: 0.6615 (ttm-80) REVERT: G 95 MET cc_start: 0.6864 (mtp) cc_final: 0.6612 (ttm) REVERT: G 231 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7805 (pp20) REVERT: H 60 PHE cc_start: 0.7504 (m-80) cc_final: 0.7125 (m-80) REVERT: H 112 MET cc_start: 0.4450 (ttm) cc_final: 0.3820 (mtm) REVERT: H 231 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6870 (pp20) outliers start: 50 outliers final: 32 residues processed: 380 average time/residue: 0.8893 time to fit residues: 395.0730 Evaluate side-chains 378 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 338 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 604 SER Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 250 optimal weight: 4.9990 chunk 406 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 360 optimal weight: 2.9990 chunk 303 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 363 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.171965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103640 restraints weight = 38489.685| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.74 r_work: 0.3155 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36606 Z= 0.186 Angle : 0.565 14.145 49943 Z= 0.300 Chirality : 0.044 0.327 5681 Planarity : 0.004 0.061 6095 Dihedral : 15.734 177.719 5808 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.37 % Allowed : 19.20 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 4194 helix: 1.10 (0.13), residues: 1695 sheet: -0.44 (0.22), residues: 492 loop : -0.34 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 77 TYR 0.034 0.001 TYR F 148 PHE 0.046 0.002 PHE H 7 TRP 0.014 0.001 TRP D1193 HIS 0.009 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (36598) covalent geometry : angle 0.56359 / 0.30 (49931) hydrogen bonds : bond 0.03841 / 2.63 ( 1632) hydrogen bonds : angle 4.42795 / 3.07 ( 4567) metal coordination : bond 0.00630 / 0.32 ( 8) metal coordination : angle 2.34244 / 1.24 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 338 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 THR cc_start: 0.8413 (t) cc_final: 0.8191 (m) REVERT: A 137 ASN cc_start: 0.8409 (m-40) cc_final: 0.8149 (m-40) REVERT: B 6 THR cc_start: 0.8466 (p) cc_final: 0.8044 (m) REVERT: B 18 GLN cc_start: 0.8442 (mt0) cc_final: 0.7913 (mm-40) REVERT: B 58 GLU cc_start: 0.8590 (pt0) cc_final: 0.8112 (pt0) REVERT: B 104 LYS cc_start: 0.7227 (tptm) cc_final: 0.6861 (tptp) REVERT: B 231 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: C 20 GLN cc_start: 0.8214 (mt0) cc_final: 0.7610 (tm-30) REVERT: C 90 VAL cc_start: 0.8647 (p) cc_final: 0.8390 (m) REVERT: C 239 MET cc_start: 0.5441 (OUTLIER) cc_final: 0.5022 (tmm) REVERT: C 350 THR cc_start: 0.8157 (m) cc_final: 0.7598 (p) REVERT: C 386 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7471 (tm-30) REVERT: C 439 LYS cc_start: 0.8105 (mttm) cc_final: 0.7732 (mtmt) REVERT: C 515 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.7490 (tmm) REVERT: C 641 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7698 (pt0) REVERT: C 779 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7998 (ttt-90) REVERT: C 834 GLN cc_start: 0.8670 (mt0) cc_final: 0.8232 (tt0) REVERT: C 943 LYS cc_start: 0.8378 (mtpp) cc_final: 0.7876 (ptmt) REVERT: C 955 GLN cc_start: 0.8072 (tp40) cc_final: 0.7688 (tp40) REVERT: C 1171 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7395 (ttp-110) REVERT: C 1219 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: D 140 TYR cc_start: 0.7975 (m-10) cc_final: 0.7738 (m-10) REVERT: D 148 GLU cc_start: 0.8491 (pt0) cc_final: 0.7971 (pp20) REVERT: D 158 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: D 162 GLU cc_start: 0.8455 (tp30) cc_final: 0.8161 (tm-30) REVERT: D 192 MET cc_start: 0.7753 (ptm) cc_final: 0.7448 (ptm) REVERT: D 293 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7482 (mtm110) REVERT: D 312 ARG cc_start: 0.7479 (ttp-170) cc_final: 0.6755 (tmt90) REVERT: D 516 ASP cc_start: 0.8319 (p0) cc_final: 0.8100 (p0) REVERT: D 666 GLU cc_start: 0.6911 (pp20) cc_final: 0.6620 (pp20) REVERT: D 707 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7845 (tt) REVERT: D 901 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8308 (ttm170) REVERT: D 1040 MET cc_start: 0.2517 (ptt) cc_final: 0.2060 (pmt) REVERT: D 1095 MET cc_start: 0.6324 (tmm) cc_final: 0.5903 (tpp) REVERT: D 1231 ARG cc_start: 0.7384 (ttp-110) cc_final: 0.7040 (ttm170) REVERT: D 1327 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: E 11 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7455 (mt-10) REVERT: E 56 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8028 (mt-10) REVERT: E 67 ARG cc_start: 0.7187 (mtt90) cc_final: 0.6901 (mtt90) REVERT: F 160 ASP cc_start: 0.8021 (t0) cc_final: 0.7468 (p0) REVERT: F 273 MET cc_start: 0.7252 (tpt) cc_final: 0.6282 (tpt) REVERT: F 277 MET cc_start: 0.7456 (tmm) cc_final: 0.6966 (mmm) REVERT: F 354 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7529 (p) REVERT: F 581 ASP cc_start: 0.7894 (t0) cc_final: 0.7399 (m-30) REVERT: F 604 SER cc_start: 0.7571 (OUTLIER) cc_final: 0.6696 (m) REVERT: G 56 ARG cc_start: 0.6863 (ttp-170) cc_final: 0.6516 (ttm-80) REVERT: G 95 MET cc_start: 0.6743 (mtp) cc_final: 0.6480 (ttm) REVERT: G 231 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7797 (pp20) REVERT: H 60 PHE cc_start: 0.7453 (m-80) cc_final: 0.7101 (m-80) REVERT: H 231 GLU cc_start: 0.7786 (mm-30) cc_final: 0.6888 (pp20) outliers start: 50 outliers final: 31 residues processed: 371 average time/residue: 0.8803 time to fit residues: 382.6004 Evaluate side-chains 376 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 604 SER Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 257 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 391 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 304 optimal weight: 5.9990 chunk 313 optimal weight: 3.9990 chunk 415 optimal weight: 4.9990 chunk 414 optimal weight: 10.0000 chunk 364 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.171517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.102970 restraints weight = 38207.208| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.76 r_work: 0.3146 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 36606 Z= 0.196 Angle : 0.577 15.011 49943 Z= 0.306 Chirality : 0.045 0.328 5681 Planarity : 0.004 0.063 6095 Dihedral : 15.783 177.473 5808 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.34 % Allowed : 19.45 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.26 (0.13), residues: 4194 helix: 1.05 (0.13), residues: 1689 sheet: -0.56 (0.22), residues: 490 loop : -0.31 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 77 TYR 0.040 0.001 TYR F 148 PHE 0.040 0.002 PHE H 7 TRP 0.013 0.001 TRP D1193 HIS 0.011 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (36598) covalent geometry : angle 0.57568 / 0.31 (49931) hydrogen bonds : bond 0.03906 / 2.68 ( 1632) hydrogen bonds : angle 4.47840 / 3.11 ( 4567) metal coordination : bond 0.00656 / 0.33 ( 8) metal coordination : angle 2.29908 / 1.21 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20271.04 seconds wall clock time: 343 minutes 44.26 seconds (20624.26 seconds total)