Starting phenix.real_space_refine on Sat Feb 7 22:35:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0x_62727/02_2026/9l0x_62727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0x_62727/02_2026/9l0x_62727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l0x_62727/02_2026/9l0x_62727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0x_62727/02_2026/9l0x_62727.map" model { file = "/net/cci-nas-00/data/ceres_data/9l0x_62727/02_2026/9l0x_62727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0x_62727/02_2026/9l0x_62727.cif" } resolution = 3.22 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 275 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 146 5.49 5 S 147 5.16 5 C 22422 2.51 5 N 6541 2.21 5 O 7263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36519 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1490 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "2" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1516 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10560 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 10369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10369 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1280} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3977 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 65} Chain breaks: 1 Chain: "G" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1026 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "H" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 879 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1074 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Time building chain proxies: 8.20, per 1000 atoms: 0.22 Number of scatterers: 36519 At special positions: 0 Unit cell: (211.2, 181.2, 180, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 147 16.00 P 146 15.00 O 7263 8.00 N 6541 7.00 C 22422 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: 3.22 Conformation dependent library (CDL) restraints added in 1.4 seconds 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7914 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 44 sheets defined 48.0% alpha, 12.9% beta 52 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'A' and resid 34 through 48 removed outlier: 3.548A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.767A 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 162 removed outlier: 4.335A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.130A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.557A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.534A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (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 229 removed outlier: 3.850A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.827A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.713A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.642A 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 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.814A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.790A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.411A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.677A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.515A pdb=" N ILE C 493 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 4.009A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.685A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 4.080A 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 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.859A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 713 removed outlier: 3.756A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 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 976 removed outlier: 3.594A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 993 through 998 removed outlier: 4.154A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1024 removed outlier: 3.645A pdb=" N GLN C1008 " --> pdb=" O ASP C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1038 Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.665A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1109 through 1135 removed outlier: 3.525A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.629A pdb=" N ASP C1150 " --> pdb=" O GLN C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.974A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 4.155A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.541A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.600A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.783A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG D 202 " --> pdb=" O CYS D 198 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.096A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 4.118A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.514A pdb=" N LEU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 3.986A 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: 3.830A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.648A pdb=" N GLU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.017A 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: 3.975A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.640A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.571A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 834 through 839' Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.074A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1138 through 1147 removed outlier: 4.573A pdb=" N LEU D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.810A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.509A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1291 removed outlier: 4.424A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D1290 " --> pdb=" O LYS D1286 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.672A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.580A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 3.800A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 removed outlier: 4.004A pdb=" N VAL E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 32 removed outlier: 3.870A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.941A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 80 removed outlier: 3.519A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 89 removed outlier: 3.553A pdb=" N SER F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 114 through 136 removed outlier: 3.600A pdb=" N GLU F 136 " --> pdb=" O CYS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 153 removed outlier: 4.228A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 213 through 231 removed outlier: 3.912A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 237 removed outlier: 3.740A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 Processing helix chain 'F' and resid 262 through 291 removed outlier: 3.797A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 298 through 307 removed outlier: 4.035A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 removed outlier: 3.681A pdb=" N ILE F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.725A pdb=" N LYS F 329 " --> pdb=" O PRO F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 removed outlier: 5.093A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU F 341 " --> pdb=" O VAL F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 382 removed outlier: 3.751A pdb=" N ILE F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 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 401 through 419 removed outlier: 3.602A pdb=" N ILE F 405 " --> pdb=" O PHE F 401 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.957A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.613A pdb=" N GLU F 473 " --> pdb=" O GLN F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 removed outlier: 3.527A pdb=" N ALA F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 500 removed outlier: 3.656A pdb=" N ILE F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F 500 " --> pdb=" O LYS F 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.636A 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 564 Processing helix chain 'F' and resid 572 through 578 Processing helix chain 'F' and resid 583 through 600 removed outlier: 3.869A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 608 removed outlier: 4.606A pdb=" N LEU F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 609 through 611 No H-bonds generated for 'chain 'F' and resid 609 through 611' Processing helix chain 'P' and resid 256 through 260 removed outlier: 3.702A pdb=" N ASP P 259 " --> pdb=" O PRO P 256 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU P 260 " --> pdb=" O VAL P 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 256 through 260' Processing helix chain 'P' and resid 263 through 272 Processing helix chain 'P' and resid 277 through 284 removed outlier: 4.343A pdb=" N LEU P 281 " --> pdb=" O TYR P 277 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 290 removed outlier: 3.920A pdb=" N LEU P 289 " --> pdb=" O THR P 285 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU P 290 " --> pdb=" O GLU P 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 285 through 290' Processing helix chain 'P' and resid 303 through 310 Processing helix chain 'G' and resid 4 through 8 removed outlier: 3.922A pdb=" N HIS G 8 " --> pdb=" O LEU G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 17 removed outlier: 3.710A pdb=" N ARG G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 23 through 28 removed outlier: 4.207A pdb=" N LEU G 27 " --> pdb=" O PRO G 23 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 23 through 28' Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 32 through 49 removed outlier: 3.981A pdb=" N VAL G 36 " --> pdb=" O PRO G 32 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU G 38 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG G 48 " --> pdb=" O ASN G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 70 removed outlier: 4.186A pdb=" N ALA G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 65 " --> pdb=" O GLN G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 95 removed outlier: 4.217A pdb=" N LEU G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 108 removed outlier: 3.541A pdb=" N ARG G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 121 Processing helix chain 'G' and resid 122 through 127 Processing helix chain 'H' and resid 27 through 31 Processing helix chain 'H' and resid 33 through 49 removed outlier: 3.551A pdb=" N ILE H 39 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL H 41 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 70 Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.571A pdb=" N ALA H 85 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 108 Processing helix chain 'H' and resid 110 through 130 Processing helix chain 'I' and resid 25 through 30 removed outlier: 4.088A pdb=" N ARG I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 50 removed outlier: 3.512A pdb=" N ILE I 39 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP I 40 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL I 41 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 70 removed outlier: 3.815A pdb=" N LEU I 65 " --> pdb=" O GLN I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 95 removed outlier: 3.871A pdb=" N ALA I 85 " --> pdb=" O THR I 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU I 86 " --> pdb=" O ILE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 108 Processing helix chain 'I' and resid 110 through 130 Processing helix chain 'J' and resid 4 through 9 removed outlier: 3.800A pdb=" N HIS J 8 " --> pdb=" O ASP J 4 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP J 9 " --> pdb=" O LEU J 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 4 through 9' Processing helix chain 'J' and resid 9 through 17 Processing helix chain 'J' and resid 18 through 22 Processing helix chain 'J' and resid 23 through 30 removed outlier: 3.766A pdb=" N LEU J 27 " --> pdb=" O PRO J 23 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG J 30 " --> pdb=" O GLU J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 49 removed outlier: 3.715A pdb=" N VAL J 36 " --> pdb=" O PRO J 32 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP J 40 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG J 48 " --> pdb=" O ASN J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 70 removed outlier: 3.594A pdb=" N LYS J 60 " --> pdb=" O GLU J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 95 Processing helix chain 'J' and resid 99 through 107 Processing helix chain 'J' and resid 110 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 4.863A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 6.700A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.973A 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: 6.831A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.615A 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 12 through 17 removed outlier: 4.845A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 8.456A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 4.185A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, 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=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.651A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 287 removed outlier: 4.414A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 256 removed outlier: 6.989A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.759A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.632A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 718 removed outlier: 6.435A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.445A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.601A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.539A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.101A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD3, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.705A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.622A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.285A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 removed outlier: 4.705A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.562A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 991 through 996 removed outlier: 6.486A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1024 through 1026 removed outlier: 3.558A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1077 through 1079 removed outlier: 3.732A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1186 through 1189 removed outlier: 3.529A pdb=" N GLU D1188 " --> pdb=" O LEU D1175 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 4.240A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) 1501 hydrogen bonds defined for protein. 4266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 10.79 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10138 1.33 - 1.45: 6527 1.45 - 1.57: 20176 1.57 - 1.70: 291 1.70 - 1.82: 250 Bond restraints: 37382 Sorted by residual: bond pdb=" N GLN H 111 " pdb=" CA GLN H 111 " ideal model delta sigma weight residual 1.462 1.490 -0.028 9.50e-03 1.11e+04 8.71e+00 bond pdb=" N VAL H 35 " pdb=" CA VAL H 35 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.30e+00 bond pdb=" N GLN I 111 " pdb=" CA GLN I 111 " ideal model delta sigma weight residual 1.462 1.489 -0.027 9.50e-03 1.11e+04 8.30e+00 bond pdb=" C1' DA 2 26 " pdb=" N9 DA 2 26 " ideal model delta sigma weight residual 1.460 1.403 0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" C1' DA 2 27 " pdb=" N9 DA 2 27 " ideal model delta sigma weight residual 1.460 1.403 0.057 2.00e-02 2.50e+03 8.13e+00 ... (remaining 37377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 50130 2.32 - 4.65: 871 4.65 - 6.97: 75 6.97 - 9.29: 22 9.29 - 11.62: 7 Bond angle restraints: 51105 Sorted by residual: angle pdb=" N ILE D 124 " pdb=" CA ILE D 124 " pdb=" C ILE D 124 " ideal model delta sigma weight residual 113.71 107.07 6.64 9.50e-01 1.11e+00 4.89e+01 angle pdb=" CA PRO G 25 " pdb=" N PRO G 25 " pdb=" CD PRO G 25 " ideal model delta sigma weight residual 112.00 104.79 7.21 1.40e+00 5.10e-01 2.65e+01 angle pdb=" C ARG G 30 " pdb=" N TRP G 31 " pdb=" CA TRP G 31 " ideal model delta sigma weight residual 123.15 112.49 10.66 2.23e+00 2.01e-01 2.28e+01 angle pdb=" O3' DA 1 6 " pdb=" C3' DA 1 6 " pdb=" C2' DA 1 6 " ideal model delta sigma weight residual 111.50 104.37 7.13 1.50e+00 4.44e-01 2.26e+01 angle pdb=" O3' DA 2 35 " pdb=" C3' DA 2 35 " pdb=" C2' DA 2 35 " ideal model delta sigma weight residual 111.50 104.95 6.55 1.50e+00 4.44e-01 1.91e+01 ... (remaining 51100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 21382 35.30 - 70.60: 1247 70.60 - 105.89: 45 105.89 - 141.19: 2 141.19 - 176.49: 3 Dihedral angle restraints: 22679 sinusoidal: 10427 harmonic: 12252 Sorted by residual: dihedral pdb=" C4' DG 2 42 " pdb=" C3' DG 2 42 " pdb=" O3' DG 2 42 " pdb=" P DA 2 43 " ideal model delta sinusoidal sigma weight residual -140.00 36.49 -176.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG 1 9 " pdb=" C3' DG 1 9 " pdb=" O3' DG 1 9 " pdb=" P DA 1 10 " ideal model delta sinusoidal sigma weight residual -140.00 32.61 -172.61 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC 2 34 " pdb=" C3' DC 2 34 " pdb=" O3' DC 2 34 " pdb=" P DA 2 35 " ideal model delta sinusoidal sigma weight residual 220.00 57.77 162.23 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 22676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4492 0.051 - 0.101: 1051 0.101 - 0.152: 227 0.152 - 0.202: 19 0.202 - 0.253: 7 Chirality restraints: 5796 Sorted by residual: chirality pdb=" CB THR C 164 " pdb=" CA THR C 164 " pdb=" OG1 THR C 164 " pdb=" CG2 THR C 164 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CG LEU P 281 " pdb=" CB LEU P 281 " pdb=" CD1 LEU P 281 " pdb=" CD2 LEU P 281 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE D 624 " pdb=" CA ILE D 624 " pdb=" CG1 ILE D 624 " pdb=" CG2 ILE D 624 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 5793 not shown) Planarity restraints: 6173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 53 " -0.061 5.00e-02 4.00e+02 9.00e-02 1.30e+01 pdb=" N PRO I 54 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO I 54 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO I 54 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1316 " 0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO C1317 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO C1317 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C1317 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 24 " 0.048 5.00e-02 4.00e+02 6.93e-02 7.69e+00 pdb=" N PRO G 25 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 25 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 25 " 0.039 5.00e-02 4.00e+02 ... (remaining 6170 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1353 2.70 - 3.25: 36996 3.25 - 3.80: 60914 3.80 - 4.35: 76396 4.35 - 4.90: 122629 Nonbonded interactions: 298288 Sorted by model distance: nonbonded pdb=" OE1 GLU D1278 " pdb=" N GLN D1279 " model vdw 2.147 3.120 nonbonded pdb=" N GLU G 28 " pdb=" OE1 GLU G 28 " model vdw 2.205 3.120 nonbonded pdb=" NZ LYS A 95 " pdb=" OD2 ASP A 120 " model vdw 2.206 3.120 nonbonded pdb=" O GLN C1288 " pdb=" OG1 THR C1292 " model vdw 2.207 3.040 nonbonded pdb=" O TYR C 3 " pdb=" NZ LYS C 8 " model vdw 2.220 3.120 ... (remaining 298283 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 6 through 233) selection = chain 'B' } ncs_group { reference = chain 'G' selection = (chain 'J' and resid 4 through 127) } ncs_group { reference = (chain 'H' and (resid 27 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 131)) selection = (chain 'I' and resid 27 through 131) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 40.760 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.005 0.118 37382 Z= 0.247 Angle : 0.723 11.618 51105 Z= 0.421 Chirality : 0.046 0.253 5796 Planarity : 0.005 0.090 6173 Dihedral : 19.280 176.491 14765 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.47 % Allowed : 23.06 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: -0.40 (0.13), residues: 4206 helix: 0.38 (0.13), residues: 1765 sheet: 0.24 (0.27), residues: 385 loop : -0.89 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 275 TYR 0.042 0.002 TYR P 277 PHE 0.045 0.002 PHE I 68 TRP 0.019 0.001 TRP F 315 HIS 0.007 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00498 (37382) covalent geometry : angle 0.72313 (51105) hydrogen bonds : bond 0.18728 ( 1623) hydrogen bonds : angle 7.31639 ( 4514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 376 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 899 GLU cc_start: 0.7679 (pt0) cc_final: 0.7418 (pt0) REVERT: C 1243 MET cc_start: 0.8751 (tpt) cc_final: 0.7972 (tpt) REVERT: D 301 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8366 (tt0) REVERT: D 410 ASP cc_start: 0.8324 (t0) cc_final: 0.8032 (t0) REVERT: D 414 GLU cc_start: 0.8786 (pp20) cc_final: 0.8479 (pp20) REVERT: D 443 GLU cc_start: 0.8222 (tp30) cc_final: 0.8002 (tp30) REVERT: D 639 VAL cc_start: 0.9419 (m) cc_final: 0.9182 (p) REVERT: D 684 ASP cc_start: 0.8493 (t0) cc_final: 0.8171 (m-30) REVERT: D 1174 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7207 (tmm-80) REVERT: F 363 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8200 (ptm-80) REVERT: I 54 PRO cc_start: 0.8836 (Cg_exo) cc_final: 0.8544 (Cg_endo) REVERT: I 98 ARG cc_start: 0.7779 (pmt-80) cc_final: 0.7568 (ptt180) REVERT: J 116 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7334 (tm-30) outliers start: 17 outliers final: 7 residues processed: 384 average time/residue: 0.2390 time to fit residues: 149.4445 Evaluate side-chains 332 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 324 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain F residue 363 ARG Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain I residue 65 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.5980 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 677 ASN C1268 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1195 GLN D1197 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 GLN J 125 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.133073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.094510 restraints weight = 90883.276| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.97 r_work: 0.3298 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37382 Z= 0.131 Angle : 0.586 10.204 51105 Z= 0.313 Chirality : 0.042 0.233 5796 Planarity : 0.004 0.063 6173 Dihedral : 17.915 175.878 6320 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.96 % Allowed : 20.97 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: -0.15 (0.13), residues: 4206 helix: 0.59 (0.13), residues: 1799 sheet: 0.39 (0.26), residues: 394 loop : -0.78 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 127 TYR 0.020 0.001 TYR F 137 PHE 0.022 0.001 PHE I 68 TRP 0.012 0.001 TRP F 315 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00289 (37382) covalent geometry : angle 0.58617 (51105) hydrogen bonds : bond 0.04355 ( 1623) hydrogen bonds : angle 5.11354 ( 4514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 397 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 275 ARG cc_start: 0.9147 (mmm160) cc_final: 0.8727 (mmm160) REVERT: C 492 MET cc_start: 0.8861 (ppp) cc_final: 0.8610 (ppp) REVERT: C 692 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8605 (m) REVERT: C 834 GLN cc_start: 0.8404 (mt0) cc_final: 0.8182 (tt0) REVERT: C 1034 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7874 (tmm-80) REVERT: C 1243 MET cc_start: 0.8824 (tpt) cc_final: 0.7999 (tpt) REVERT: D 29 MET cc_start: 0.7170 (pmm) cc_final: 0.6889 (pmm) REVERT: D 301 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8589 (tt0) REVERT: D 443 GLU cc_start: 0.8378 (tp30) cc_final: 0.8148 (tp30) REVERT: D 684 ASP cc_start: 0.8587 (t0) cc_final: 0.8249 (m-30) REVERT: D 1174 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7189 (tmm-80) REVERT: D 1189 MET cc_start: 0.7527 (tpp) cc_final: 0.7312 (tpp) REVERT: D 1260 MET cc_start: 0.8592 (mtt) cc_final: 0.8208 (mtp) REVERT: D 1278 GLU cc_start: 0.7880 (tp30) cc_final: 0.7639 (tp30) REVERT: E 56 GLU cc_start: 0.7586 (pp20) cc_final: 0.7356 (pp20) REVERT: F 456 MET cc_start: 0.8245 (mmm) cc_final: 0.7850 (mmm) REVERT: G 53 ASN cc_start: 0.9025 (p0) cc_final: 0.8803 (p0) REVERT: G 56 GLU cc_start: 0.9222 (mp0) cc_final: 0.8896 (mp0) REVERT: G 60 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8298 (mptp) REVERT: G 113 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8516 (tm-30) REVERT: I 39 ILE cc_start: 0.9205 (mp) cc_final: 0.8837 (mm) REVERT: I 75 TYR cc_start: 0.4334 (p90) cc_final: 0.4084 (p90) REVERT: I 95 PHE cc_start: 0.8277 (t80) cc_final: 0.7849 (t80) REVERT: J 39 ILE cc_start: 0.9291 (mt) cc_final: 0.9066 (tt) outliers start: 108 outliers final: 43 residues processed: 481 average time/residue: 0.2265 time to fit residues: 181.1068 Evaluate side-chains 374 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 330 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 115 TYR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 355 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 chunk 424 optimal weight: 0.2980 chunk 240 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 326 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 341 optimal weight: 0.0570 chunk 401 optimal weight: 8.9990 chunk 385 optimal weight: 6.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1236 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D1195 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.129111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.089665 restraints weight = 90520.212| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.95 r_work: 0.3254 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37382 Z= 0.144 Angle : 0.565 10.210 51105 Z= 0.301 Chirality : 0.042 0.252 5796 Planarity : 0.004 0.051 6173 Dihedral : 17.841 176.603 6312 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.76 % Allowed : 20.78 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.13), residues: 4206 helix: 0.72 (0.13), residues: 1803 sheet: 0.37 (0.26), residues: 412 loop : -0.75 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 903 TYR 0.020 0.001 TYR F 143 PHE 0.018 0.001 PHE H 74 TRP 0.015 0.001 TRP F 315 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00327 (37382) covalent geometry : angle 0.56481 (51105) hydrogen bonds : bond 0.03951 ( 1623) hydrogen bonds : angle 4.75545 ( 4514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 371 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8178 (p0) cc_final: 0.7959 (p0) REVERT: B 145 LYS cc_start: 0.7606 (tptt) cc_final: 0.7302 (tptt) REVERT: C 124 MET cc_start: 0.8829 (ptt) cc_final: 0.8477 (ptt) REVERT: C 275 ARG cc_start: 0.9168 (mmm160) cc_final: 0.8741 (mmm160) REVERT: C 317 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7265 (pp) REVERT: C 492 MET cc_start: 0.9156 (ppp) cc_final: 0.8922 (ppp) REVERT: C 834 GLN cc_start: 0.8453 (mt0) cc_final: 0.8190 (tt0) REVERT: C 1034 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7958 (tmm-80) REVERT: D 29 MET cc_start: 0.7544 (pmm) cc_final: 0.7061 (pmm) REVERT: D 66 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8180 (ttpp) REVERT: D 200 GLN cc_start: 0.8296 (tt0) cc_final: 0.7813 (tm-30) REVERT: D 301 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8571 (tt0) REVERT: D 374 LEU cc_start: 0.8156 (pp) cc_final: 0.7902 (tt) REVERT: D 443 GLU cc_start: 0.8381 (tp30) cc_final: 0.8128 (tp30) REVERT: D 639 VAL cc_start: 0.9369 (m) cc_final: 0.9165 (p) REVERT: D 684 ASP cc_start: 0.8609 (t0) cc_final: 0.8367 (m-30) REVERT: D 706 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8804 (m) REVERT: D 1059 LEU cc_start: 0.4278 (OUTLIER) cc_final: 0.3929 (mt) REVERT: D 1174 ARG cc_start: 0.7471 (ttp80) cc_final: 0.7185 (tmm-80) REVERT: D 1189 MET cc_start: 0.7362 (tpp) cc_final: 0.7067 (tpp) REVERT: D 1209 VAL cc_start: 0.8514 (t) cc_final: 0.8096 (p) REVERT: E 56 GLU cc_start: 0.7881 (pp20) cc_final: 0.7667 (pp20) REVERT: F 147 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: F 456 MET cc_start: 0.8426 (mmm) cc_final: 0.7987 (mmm) REVERT: P 275 ILE cc_start: 0.6525 (mm) cc_final: 0.6063 (mm) REVERT: P 281 LEU cc_start: 0.8781 (tt) cc_final: 0.8536 (mt) REVERT: G 56 GLU cc_start: 0.9343 (mp0) cc_final: 0.9079 (mp0) REVERT: G 60 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8398 (mptp) REVERT: G 113 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8571 (tm-30) REVERT: G 116 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7999 (pp30) REVERT: I 44 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.6774 (p0) REVERT: I 95 PHE cc_start: 0.8623 (t80) cc_final: 0.8238 (t80) REVERT: I 101 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8395 (mm-30) outliers start: 137 outliers final: 67 residues processed: 481 average time/residue: 0.2194 time to fit residues: 176.5182 Evaluate side-chains 402 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 329 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 115 TYR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 44 ASN Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 67 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 192 optimal weight: 0.8980 chunk 216 optimal weight: 0.6980 chunk 132 optimal weight: 0.0570 chunk 309 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 310 optimal weight: 4.9990 chunk 385 optimal weight: 0.7980 chunk 405 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS C1257 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN I 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.132423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095697 restraints weight = 92657.493| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.09 r_work: 0.3226 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37382 Z= 0.141 Angle : 0.559 9.910 51105 Z= 0.296 Chirality : 0.041 0.204 5796 Planarity : 0.004 0.052 6173 Dihedral : 17.799 176.799 6303 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.62 % Allowed : 20.48 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 4206 helix: 0.81 (0.13), residues: 1805 sheet: 0.41 (0.26), residues: 405 loop : -0.73 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 312 TYR 0.015 0.001 TYR C 262 PHE 0.029 0.001 PHE I 68 TRP 0.025 0.001 TRP F 315 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00325 (37382) covalent geometry : angle 0.55883 (51105) hydrogen bonds : bond 0.03621 ( 1623) hydrogen bonds : angle 4.62889 ( 4514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 363 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8136 (p0) cc_final: 0.7885 (p0) REVERT: B 145 LYS cc_start: 0.7798 (tptt) cc_final: 0.7360 (tptt) REVERT: C 124 MET cc_start: 0.8819 (ptt) cc_final: 0.8475 (ptt) REVERT: C 275 ARG cc_start: 0.9157 (mmm160) cc_final: 0.8719 (mmm160) REVERT: C 317 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7343 (pp) REVERT: C 492 MET cc_start: 0.9239 (ppp) cc_final: 0.9029 (ppp) REVERT: C 493 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7960 (tt) REVERT: C 653 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.7696 (tpt) REVERT: C 834 GLN cc_start: 0.8481 (mt0) cc_final: 0.8192 (tt0) REVERT: C 942 ASP cc_start: 0.7764 (t0) cc_final: 0.7505 (t70) REVERT: C 1034 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7950 (tmm-80) REVERT: D 29 MET cc_start: 0.7611 (pmm) cc_final: 0.7091 (pmm) REVERT: D 66 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8103 (ttpp) REVERT: D 200 GLN cc_start: 0.8122 (tt0) cc_final: 0.7876 (tm-30) REVERT: D 283 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8793 (mm) REVERT: D 301 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8622 (tt0) REVERT: D 374 LEU cc_start: 0.8455 (pp) cc_final: 0.8114 (tt) REVERT: D 443 GLU cc_start: 0.8437 (tp30) cc_final: 0.8188 (tp30) REVERT: D 513 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8613 (ptm) REVERT: D 639 VAL cc_start: 0.9407 (m) cc_final: 0.9164 (p) REVERT: D 684 ASP cc_start: 0.8595 (t0) cc_final: 0.8277 (m-30) REVERT: D 706 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8793 (m) REVERT: D 714 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5868 (pm20) REVERT: D 1059 LEU cc_start: 0.4172 (OUTLIER) cc_final: 0.3849 (mt) REVERT: D 1174 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7249 (tmm-80) REVERT: D 1189 MET cc_start: 0.7570 (tpp) cc_final: 0.7245 (tpp) REVERT: D 1209 VAL cc_start: 0.8651 (t) cc_final: 0.8272 (p) REVERT: D 1278 GLU cc_start: 0.7988 (tp30) cc_final: 0.7763 (tp30) REVERT: E 56 GLU cc_start: 0.7933 (pp20) cc_final: 0.7283 (pp20) REVERT: F 146 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: F 456 MET cc_start: 0.8455 (mmm) cc_final: 0.8070 (mmm) REVERT: P 275 ILE cc_start: 0.6407 (mm) cc_final: 0.6028 (mm) REVERT: P 281 LEU cc_start: 0.8803 (tt) cc_final: 0.8552 (mt) REVERT: G 56 GLU cc_start: 0.9303 (mp0) cc_final: 0.8871 (mp0) REVERT: G 60 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8393 (mptp) REVERT: I 95 PHE cc_start: 0.8453 (t80) cc_final: 0.8048 (t80) REVERT: I 101 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8354 (mm-30) REVERT: J 129 HIS cc_start: 0.3767 (p-80) cc_final: 0.3385 (p-80) outliers start: 132 outliers final: 75 residues processed: 470 average time/residue: 0.2141 time to fit residues: 167.7031 Evaluate side-chains 416 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 331 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 115 TYR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 122 ARG Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 33 optimal weight: 5.9990 chunk 351 optimal weight: 6.9990 chunk 399 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 289 optimal weight: 20.0000 chunk 120 optimal weight: 0.0070 chunk 259 optimal weight: 3.9990 chunk 397 optimal weight: 9.9990 chunk 331 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1236 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 268 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.131504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.094502 restraints weight = 92120.430| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.82 r_work: 0.3216 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37382 Z= 0.142 Angle : 0.558 9.392 51105 Z= 0.296 Chirality : 0.041 0.178 5796 Planarity : 0.004 0.067 6173 Dihedral : 17.779 176.615 6301 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.68 % Allowed : 20.42 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.07 (0.13), residues: 4206 helix: 0.87 (0.13), residues: 1810 sheet: 0.26 (0.26), residues: 412 loop : -0.72 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 69 TYR 0.037 0.001 TYR F 137 PHE 0.023 0.001 PHE H 74 TRP 0.035 0.001 TRP F 315 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00328 (37382) covalent geometry : angle 0.55781 (51105) hydrogen bonds : bond 0.03550 ( 1623) hydrogen bonds : angle 4.54585 ( 4514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 355 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8049 (p0) cc_final: 0.7798 (p0) REVERT: B 145 LYS cc_start: 0.8028 (tptt) cc_final: 0.7706 (tptt) REVERT: C 132 ASP cc_start: 0.8613 (t0) cc_final: 0.8406 (t0) REVERT: C 255 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8529 (mm) REVERT: C 275 ARG cc_start: 0.9169 (mmm160) cc_final: 0.8772 (mmm160) REVERT: C 315 MET cc_start: 0.8820 (tpp) cc_final: 0.8368 (tpp) REVERT: C 317 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7388 (pp) REVERT: C 492 MET cc_start: 0.9259 (ppp) cc_final: 0.9057 (ppp) REVERT: C 493 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8034 (tt) REVERT: C 653 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.7614 (tpt) REVERT: C 800 MET cc_start: 0.8279 (pmm) cc_final: 0.7779 (ptp) REVERT: C 834 GLN cc_start: 0.8468 (mt0) cc_final: 0.8181 (tt0) REVERT: C 942 ASP cc_start: 0.7769 (t0) cc_final: 0.7524 (t70) REVERT: C 1034 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7940 (tmm-80) REVERT: C 1066 MET cc_start: 0.8599 (mtp) cc_final: 0.8390 (mtp) REVERT: C 1135 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: C 1194 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8728 (mt-10) REVERT: D 29 MET cc_start: 0.7502 (pmm) cc_final: 0.7063 (pmm) REVERT: D 66 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8128 (ttpp) REVERT: D 151 MET cc_start: 0.6358 (ptp) cc_final: 0.5946 (ptp) REVERT: D 175 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: D 197 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: D 200 GLN cc_start: 0.8187 (tt0) cc_final: 0.7948 (tm-30) REVERT: D 283 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8804 (mm) REVERT: D 301 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8710 (tt0) REVERT: D 374 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8176 (tt) REVERT: D 443 GLU cc_start: 0.8401 (tp30) cc_final: 0.8132 (tp30) REVERT: D 684 ASP cc_start: 0.8682 (t0) cc_final: 0.8324 (m-30) REVERT: D 706 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8844 (m) REVERT: D 707 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7811 (pt) REVERT: D 714 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.5836 (pm20) REVERT: D 801 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8862 (t) REVERT: D 1059 LEU cc_start: 0.4258 (OUTLIER) cc_final: 0.3942 (mt) REVERT: D 1174 ARG cc_start: 0.7732 (ttp80) cc_final: 0.7353 (tmm-80) REVERT: D 1189 MET cc_start: 0.7574 (tpp) cc_final: 0.7197 (tpp) REVERT: D 1209 VAL cc_start: 0.8736 (t) cc_final: 0.8386 (p) REVERT: D 1278 GLU cc_start: 0.8109 (tp30) cc_final: 0.7819 (tp30) REVERT: E 56 GLU cc_start: 0.8101 (pp20) cc_final: 0.7569 (pp20) REVERT: F 146 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: F 273 MET cc_start: 0.9098 (mmp) cc_final: 0.8819 (mmp) REVERT: F 456 MET cc_start: 0.8461 (mmm) cc_final: 0.8098 (mmm) REVERT: F 598 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9212 (mm) REVERT: P 275 ILE cc_start: 0.6346 (mm) cc_final: 0.5922 (mm) REVERT: P 277 TYR cc_start: 0.5901 (m-80) cc_final: 0.5516 (m-80) REVERT: P 281 LEU cc_start: 0.8814 (tt) cc_final: 0.8575 (mt) REVERT: G 56 GLU cc_start: 0.9338 (mp0) cc_final: 0.8874 (mp0) REVERT: G 60 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8391 (mptp) REVERT: G 113 GLN cc_start: 0.8573 (tp40) cc_final: 0.8275 (tm-30) REVERT: G 116 GLN cc_start: 0.8418 (tm-30) cc_final: 0.7987 (pp30) REVERT: I 101 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8435 (mm-30) outliers start: 134 outliers final: 70 residues processed: 465 average time/residue: 0.2217 time to fit residues: 172.1108 Evaluate side-chains 424 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 336 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1135 GLN Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 115 TYR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 408 optimal weight: 1.9990 chunk 370 optimal weight: 0.0670 chunk 46 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 chunk 420 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 932 GLN C1257 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1366 HIS F 409 ASN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN J 21 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.124151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084693 restraints weight = 89610.543| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.87 r_work: 0.3115 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 37382 Z= 0.223 Angle : 0.631 9.811 51105 Z= 0.334 Chirality : 0.044 0.209 5796 Planarity : 0.004 0.057 6173 Dihedral : 17.905 178.193 6301 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.53 % Allowed : 20.34 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4206 helix: 0.75 (0.13), residues: 1828 sheet: 0.13 (0.25), residues: 428 loop : -0.73 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 478 TYR 0.025 0.002 TYR C 756 PHE 0.022 0.002 PHE J 6 TRP 0.037 0.002 TRP F 315 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00524 (37382) covalent geometry : angle 0.63136 (51105) hydrogen bonds : bond 0.04166 ( 1623) hydrogen bonds : angle 4.65181 ( 4514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 336 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8166 (p0) cc_final: 0.7953 (p0) REVERT: A 207 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7799 (t) REVERT: B 142 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.7962 (pmm) REVERT: B 145 LYS cc_start: 0.8181 (tptt) cc_final: 0.7834 (tptt) REVERT: C 132 ASP cc_start: 0.8703 (t0) cc_final: 0.8475 (t0) REVERT: C 200 ARG cc_start: 0.8439 (tpp-160) cc_final: 0.8052 (tpp-160) REVERT: C 255 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8534 (mm) REVERT: C 275 ARG cc_start: 0.9188 (mmm160) cc_final: 0.8806 (mmm160) REVERT: C 317 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7639 (pp) REVERT: C 492 MET cc_start: 0.9231 (ppp) cc_final: 0.9027 (ppp) REVERT: C 653 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.7529 (tpt) REVERT: C 1034 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8055 (tmm-80) REVERT: C 1113 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8889 (mt) REVERT: C 1135 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: C 1194 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: C 1222 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: C 1243 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8375 (tpt) REVERT: D 66 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8416 (ttpp) REVERT: D 175 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: D 200 GLN cc_start: 0.8304 (tt0) cc_final: 0.8046 (tm-30) REVERT: D 283 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8840 (mm) REVERT: D 374 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8271 (tt) REVERT: D 443 GLU cc_start: 0.8524 (tp30) cc_final: 0.8229 (tp30) REVERT: D 684 ASP cc_start: 0.8744 (t0) cc_final: 0.8369 (m-30) REVERT: D 707 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7974 (pt) REVERT: D 714 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5168 (pm20) REVERT: D 1059 LEU cc_start: 0.4340 (OUTLIER) cc_final: 0.4033 (mt) REVERT: D 1174 ARG cc_start: 0.7644 (ttp80) cc_final: 0.7311 (tmm-80) REVERT: D 1189 MET cc_start: 0.7716 (tpp) cc_final: 0.7301 (tpp) REVERT: D 1209 VAL cc_start: 0.8949 (t) cc_final: 0.8678 (p) REVERT: D 1278 GLU cc_start: 0.8116 (tp30) cc_final: 0.7879 (tp30) REVERT: D 1282 TYR cc_start: 0.8298 (m-80) cc_final: 0.7879 (m-80) REVERT: E 64 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.4963 (tt) REVERT: F 146 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: F 148 TYR cc_start: 0.6822 (t80) cc_final: 0.6568 (t80) REVERT: P 275 ILE cc_start: 0.6416 (mm) cc_final: 0.5808 (mm) REVERT: P 277 TYR cc_start: 0.5813 (m-80) cc_final: 0.5384 (m-80) REVERT: G 56 GLU cc_start: 0.9368 (mp0) cc_final: 0.8883 (mp0) REVERT: G 60 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8693 (mmtt) REVERT: G 113 GLN cc_start: 0.8642 (tp40) cc_final: 0.8236 (tm-30) REVERT: G 116 GLN cc_start: 0.8504 (tm-30) cc_final: 0.7964 (pp30) REVERT: I 75 TYR cc_start: 0.4916 (p90) cc_final: 0.3612 (p90) REVERT: I 123 LYS cc_start: 0.9584 (mmmt) cc_final: 0.9369 (mmmm) outliers start: 165 outliers final: 93 residues processed: 476 average time/residue: 0.2147 time to fit residues: 172.0979 Evaluate side-chains 423 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 311 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1135 GLN Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 714 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 455 HIS Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 115 TYR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 69 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 426 optimal weight: 5.9990 chunk 407 optimal weight: 6.9990 chunk 346 optimal weight: 7.9990 chunk 421 optimal weight: 10.0000 chunk 293 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 196 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 343 optimal weight: 5.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1236 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS F 258 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN ** I 130 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 = 0.4026 r_free = 0.4026 target = 0.125335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086314 restraints weight = 89397.691| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.88 r_work: 0.3144 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 37382 Z= 0.164 Angle : 0.592 10.603 51105 Z= 0.312 Chirality : 0.042 0.193 5796 Planarity : 0.004 0.047 6173 Dihedral : 17.892 178.202 6301 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.95 % Allowed : 21.05 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.06 (0.13), residues: 4206 helix: 0.82 (0.13), residues: 1824 sheet: 0.18 (0.26), residues: 416 loop : -0.68 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 478 TYR 0.026 0.001 TYR F 143 PHE 0.033 0.002 PHE H 68 TRP 0.042 0.001 TRP F 315 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00384 (37382) covalent geometry : angle 0.59203 (51105) hydrogen bonds : bond 0.03720 ( 1623) hydrogen bonds : angle 4.60597 ( 4514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 344 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.7791 (pmm) REVERT: B 227 GLN cc_start: 0.8506 (tt0) cc_final: 0.8292 (tt0) REVERT: C 85 CYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8692 (m) REVERT: C 132 ASP cc_start: 0.8720 (t0) cc_final: 0.8504 (t0) REVERT: C 255 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8585 (mm) REVERT: C 275 ARG cc_start: 0.9190 (mmm160) cc_final: 0.8813 (mmm160) REVERT: C 317 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7669 (pp) REVERT: C 493 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8119 (tt) REVERT: C 653 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.7578 (tpt) REVERT: C 834 GLN cc_start: 0.8519 (mt0) cc_final: 0.8194 (tt0) REVERT: C 1034 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7981 (tmm-80) REVERT: C 1135 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: C 1194 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: D 66 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8332 (ttpp) REVERT: D 200 GLN cc_start: 0.8296 (tt0) cc_final: 0.8038 (tm-30) REVERT: D 283 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8811 (mm) REVERT: D 374 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8195 (tt) REVERT: D 443 GLU cc_start: 0.8541 (tp30) cc_final: 0.8250 (tp30) REVERT: D 1059 LEU cc_start: 0.4208 (OUTLIER) cc_final: 0.3901 (mt) REVERT: D 1174 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7357 (tmm-80) REVERT: D 1189 MET cc_start: 0.7822 (tpp) cc_final: 0.7261 (tpp) REVERT: D 1209 VAL cc_start: 0.8966 (t) cc_final: 0.8723 (p) REVERT: D 1278 GLU cc_start: 0.8114 (tp30) cc_final: 0.7905 (tp30) REVERT: D 1282 TYR cc_start: 0.8253 (m-80) cc_final: 0.7782 (m-80) REVERT: E 69 ARG cc_start: 0.7843 (ptp90) cc_final: 0.7325 (ptt180) REVERT: F 146 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: F 148 TYR cc_start: 0.6814 (t80) cc_final: 0.6548 (t80) REVERT: F 273 MET cc_start: 0.9101 (mmp) cc_final: 0.8865 (mmp) REVERT: G 56 GLU cc_start: 0.9400 (mp0) cc_final: 0.9103 (mp0) REVERT: G 60 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8685 (mmtt) REVERT: G 113 GLN cc_start: 0.8680 (tp40) cc_final: 0.8240 (tm-30) REVERT: I 75 TYR cc_start: 0.4609 (p90) cc_final: 0.3536 (p90) REVERT: I 123 LYS cc_start: 0.9601 (mmmt) cc_final: 0.9401 (mmmm) outliers start: 144 outliers final: 92 residues processed: 465 average time/residue: 0.2248 time to fit residues: 174.3614 Evaluate side-chains 417 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 312 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1135 GLN Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1204 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 115 TYR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 86 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 349 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 343 optimal weight: 7.9990 chunk 420 optimal weight: 10.0000 chunk 284 optimal weight: 7.9990 chunk 389 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 387 optimal weight: 8.9990 chunk 280 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 604 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN J 53 ASN ** J 73 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 = 0.3888 r_free = 0.3888 target = 0.117470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.077720 restraints weight = 87568.754| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.70 r_work: 0.2998 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 37382 Z= 0.312 Angle : 0.721 10.783 51105 Z= 0.379 Chirality : 0.047 0.188 5796 Planarity : 0.005 0.067 6173 Dihedral : 18.146 179.504 6301 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.12 % Allowed : 21.27 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: -0.20 (0.13), residues: 4206 helix: 0.58 (0.12), residues: 1835 sheet: -0.11 (0.25), residues: 406 loop : -0.75 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 28 TYR 0.032 0.002 TYR F 143 PHE 0.039 0.002 PHE I 74 TRP 0.051 0.003 TRP H 31 HIS 0.007 0.001 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00738 (37382) covalent geometry : angle 0.72051 (51105) hydrogen bonds : bond 0.04783 ( 1623) hydrogen bonds : angle 4.84933 ( 4514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 325 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7404 (p-80) REVERT: A 207 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7965 (t) REVERT: B 142 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8145 (pmm) REVERT: C 255 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8512 (mm) REVERT: C 275 ARG cc_start: 0.9166 (mmm160) cc_final: 0.8769 (mmm160) REVERT: C 317 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8281 (pp) REVERT: C 653 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8052 (ttt) REVERT: C 708 VAL cc_start: 0.9151 (p) cc_final: 0.8926 (t) REVERT: C 1034 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7938 (tmm-80) REVERT: C 1113 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9030 (mt) REVERT: C 1135 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7911 (pm20) REVERT: C 1157 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: C 1194 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: C 1222 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: C 1243 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8375 (tpt) REVERT: D 66 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8431 (ttpp) REVERT: D 200 GLN cc_start: 0.8399 (tt0) cc_final: 0.8148 (tm-30) REVERT: D 283 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8938 (mm) REVERT: D 443 GLU cc_start: 0.8498 (tp30) cc_final: 0.8260 (tp30) REVERT: D 513 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9078 (ptm) REVERT: D 684 ASP cc_start: 0.8620 (t0) cc_final: 0.8365 (t0) REVERT: D 1174 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7132 (tmm-80) REVERT: D 1189 MET cc_start: 0.7858 (tpp) cc_final: 0.7287 (tpp) REVERT: E 65 ASP cc_start: 0.8376 (m-30) cc_final: 0.7953 (m-30) REVERT: F 146 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: F 148 TYR cc_start: 0.6894 (t80) cc_final: 0.6613 (t80) REVERT: F 273 MET cc_start: 0.9038 (mmp) cc_final: 0.8787 (mmp) REVERT: G 56 GLU cc_start: 0.9353 (mp0) cc_final: 0.9042 (mp0) REVERT: G 60 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8649 (mmtt) REVERT: G 113 GLN cc_start: 0.8712 (tp40) cc_final: 0.8111 (tm-30) REVERT: G 116 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7884 (pp30) REVERT: I 47 LYS cc_start: 0.8615 (tttt) cc_final: 0.8353 (tmtt) REVERT: I 75 TYR cc_start: 0.4525 (p90) cc_final: 0.3831 (p90) outliers start: 150 outliers final: 100 residues processed: 449 average time/residue: 0.2006 time to fit residues: 151.6684 Evaluate side-chains 417 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 301 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1135 GLN Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1222 GLU Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1204 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 115 TYR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 91 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 156 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 228 optimal weight: 0.0000 chunk 430 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 354 optimal weight: 1.9990 chunk 429 optimal weight: 10.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN F 227 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN ** J 73 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 = 0.3938 r_free = 0.3938 target = 0.120957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.082146 restraints weight = 88269.502| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.03 r_work: 0.3051 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37382 Z= 0.148 Angle : 0.612 10.896 51105 Z= 0.323 Chirality : 0.042 0.195 5796 Planarity : 0.004 0.051 6173 Dihedral : 18.018 179.269 6301 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.96 % Allowed : 22.70 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.01 (0.13), residues: 4206 helix: 0.75 (0.12), residues: 1830 sheet: 0.07 (0.26), residues: 387 loop : -0.64 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 478 TYR 0.031 0.001 TYR F 143 PHE 0.028 0.001 PHE I 95 TRP 0.040 0.002 TRP H 31 HIS 0.008 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00344 (37382) covalent geometry : angle 0.61222 (51105) hydrogen bonds : bond 0.03752 ( 1623) hydrogen bonds : angle 4.67266 ( 4514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 337 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.7996 (pmm) REVERT: B 227 GLN cc_start: 0.8566 (tt0) cc_final: 0.8304 (tt0) REVERT: C 100 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8674 (pp) REVERT: C 200 ARG cc_start: 0.8481 (tpp-160) cc_final: 0.7847 (tpp-160) REVERT: C 255 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8583 (mm) REVERT: C 275 ARG cc_start: 0.9150 (mmm160) cc_final: 0.8823 (mmm160) REVERT: C 493 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8208 (tt) REVERT: C 653 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.7585 (tpt) REVERT: C 834 GLN cc_start: 0.8496 (mt0) cc_final: 0.8195 (tt0) REVERT: C 1034 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7855 (tmm-80) REVERT: C 1135 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: C 1194 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: C 1304 MET cc_start: 0.8937 (tpt) cc_final: 0.8438 (tpt) REVERT: D 66 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8359 (ttpp) REVERT: D 200 GLN cc_start: 0.8312 (tt0) cc_final: 0.8069 (tm-30) REVERT: D 283 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8841 (mm) REVERT: D 374 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8230 (tt) REVERT: D 443 GLU cc_start: 0.8479 (tp30) cc_final: 0.8191 (tp30) REVERT: D 513 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.9053 (ptm) REVERT: D 684 ASP cc_start: 0.8643 (t0) cc_final: 0.8424 (m-30) REVERT: D 698 MET cc_start: 0.9326 (mmm) cc_final: 0.9112 (tpp) REVERT: D 1174 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7508 (tmm-80) REVERT: D 1189 MET cc_start: 0.7870 (tpp) cc_final: 0.7282 (tpp) REVERT: D 1260 MET cc_start: 0.9313 (mtp) cc_final: 0.9055 (mtm) REVERT: D 1281 GLU cc_start: 0.8436 (pm20) cc_final: 0.8197 (pm20) REVERT: D 1282 TYR cc_start: 0.8339 (m-80) cc_final: 0.7898 (m-80) REVERT: E 65 ASP cc_start: 0.8198 (m-30) cc_final: 0.7756 (m-30) REVERT: F 146 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: F 148 TYR cc_start: 0.6860 (t80) cc_final: 0.6577 (t80) REVERT: F 273 MET cc_start: 0.8988 (mmp) cc_final: 0.8778 (mmp) REVERT: P 278 ILE cc_start: 0.7019 (mm) cc_final: 0.6441 (pt) REVERT: G 56 GLU cc_start: 0.9413 (mp0) cc_final: 0.9172 (mp0) REVERT: G 60 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8692 (mmtt) REVERT: G 113 GLN cc_start: 0.8741 (tp40) cc_final: 0.8129 (tm-30) REVERT: G 116 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7921 (pp30) REVERT: I 47 LYS cc_start: 0.8650 (tttt) cc_final: 0.8391 (tmtt) REVERT: I 75 TYR cc_start: 0.4569 (p90) cc_final: 0.3947 (p90) REVERT: I 80 ASP cc_start: 0.7744 (p0) cc_final: 0.7526 (p0) REVERT: J 100 MET cc_start: 0.7044 (ttt) cc_final: 0.6642 (tmm) REVERT: J 116 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 108 outliers final: 75 residues processed: 426 average time/residue: 0.2123 time to fit residues: 151.7057 Evaluate side-chains 405 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 318 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1135 GLN Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain P residue 280 ASP Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 115 TYR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 94 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 413 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 418 optimal weight: 9.9990 chunk 376 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 266 optimal weight: 6.9990 chunk 149 optimal weight: 0.1980 chunk 174 optimal weight: 0.8980 chunk 311 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 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 = 0.3934 r_free = 0.3934 target = 0.120649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.081141 restraints weight = 88113.011| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.75 r_work: 0.3057 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37382 Z= 0.160 Angle : 0.623 15.651 51105 Z= 0.325 Chirality : 0.042 0.179 5796 Planarity : 0.004 0.051 6173 Dihedral : 17.994 177.869 6301 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.74 % Allowed : 22.87 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.07 (0.13), residues: 4206 helix: 0.80 (0.12), residues: 1827 sheet: 0.12 (0.26), residues: 396 loop : -0.62 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 88 TYR 0.032 0.001 TYR F 143 PHE 0.024 0.001 PHE C 545 TRP 0.039 0.002 TRP H 31 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00377 (37382) covalent geometry : angle 0.62310 (51105) hydrogen bonds : bond 0.03737 ( 1623) hydrogen bonds : angle 4.63375 ( 4514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 330 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7843 (t) REVERT: B 142 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.7997 (pmm) REVERT: B 227 GLN cc_start: 0.8553 (tt0) cc_final: 0.8288 (tt0) REVERT: C 100 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8628 (pp) REVERT: C 200 ARG cc_start: 0.8510 (tpp-160) cc_final: 0.8008 (tpp-160) REVERT: C 255 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8591 (mm) REVERT: C 275 ARG cc_start: 0.9227 (mmm160) cc_final: 0.8877 (mmm160) REVERT: C 493 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8143 (tt) REVERT: C 653 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.7592 (tpt) REVERT: C 834 GLN cc_start: 0.8479 (mt0) cc_final: 0.8188 (tt0) REVERT: C 1034 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7947 (tmm-80) REVERT: C 1135 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: C 1194 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: D 66 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8346 (ttpp) REVERT: D 200 GLN cc_start: 0.8365 (tt0) cc_final: 0.8102 (tm-30) REVERT: D 283 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8816 (mm) REVERT: D 374 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8215 (tt) REVERT: D 443 GLU cc_start: 0.8419 (tp30) cc_final: 0.8123 (tp30) REVERT: D 513 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.9052 (ptm) REVERT: D 684 ASP cc_start: 0.8633 (t0) cc_final: 0.8368 (t0) REVERT: D 698 MET cc_start: 0.9287 (mmm) cc_final: 0.9061 (tpp) REVERT: D 1174 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7466 (tmm-80) REVERT: D 1189 MET cc_start: 0.7921 (tpp) cc_final: 0.7208 (tpp) REVERT: D 1281 GLU cc_start: 0.8497 (pm20) cc_final: 0.8239 (pm20) REVERT: D 1282 TYR cc_start: 0.8280 (m-80) cc_final: 0.7927 (m-80) REVERT: D 1334 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8271 (mm-30) REVERT: E 69 ARG cc_start: 0.7728 (ptp90) cc_final: 0.7467 (ptp-110) REVERT: F 146 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: F 148 TYR cc_start: 0.6807 (t80) cc_final: 0.6565 (t80) REVERT: F 273 MET cc_start: 0.8999 (mmp) cc_final: 0.8600 (mmp) REVERT: F 487 MET cc_start: 0.7919 (mmm) cc_final: 0.7155 (mtp) REVERT: P 278 ILE cc_start: 0.6878 (mm) cc_final: 0.6238 (pt) REVERT: G 56 GLU cc_start: 0.9423 (mp0) cc_final: 0.9188 (mp0) REVERT: G 60 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8652 (mmtt) REVERT: G 113 GLN cc_start: 0.8725 (tp40) cc_final: 0.8126 (tm-30) REVERT: G 116 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7910 (pp30) REVERT: I 47 LYS cc_start: 0.8644 (tttt) cc_final: 0.8384 (tmtt) REVERT: I 75 TYR cc_start: 0.4616 (p90) cc_final: 0.4104 (p90) REVERT: I 111 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8359 (mp10) REVERT: J 100 MET cc_start: 0.6931 (ttt) cc_final: 0.6719 (tmm) REVERT: J 113 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7801 (pt0) outliers start: 100 outliers final: 73 residues processed: 412 average time/residue: 0.2149 time to fit residues: 147.6426 Evaluate side-chains 407 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 320 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 610 GLU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1135 GLN Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 663 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 115 TYR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 107 optimal weight: 0.0050 chunk 86 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 255 optimal weight: 0.9980 chunk 397 optimal weight: 7.9990 chunk 199 optimal weight: 0.0980 chunk 385 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 418 optimal weight: 1.9990 overall best weight: 1.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN ** J 73 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 = 0.3990 r_free = 0.3990 target = 0.122468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083007 restraints weight = 88777.344| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.87 r_work: 0.3112 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 37382 Z= 0.159 Angle : 0.614 14.865 51105 Z= 0.321 Chirality : 0.042 0.194 5796 Planarity : 0.004 0.050 6173 Dihedral : 17.970 178.251 6300 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.85 % Allowed : 22.92 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.13), residues: 4206 helix: 0.82 (0.12), residues: 1827 sheet: 0.13 (0.26), residues: 396 loop : -0.60 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 88 TYR 0.028 0.001 TYR F 143 PHE 0.021 0.001 PHE J 74 TRP 0.042 0.002 TRP F 315 HIS 0.005 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00374 (37382) covalent geometry : angle 0.61444 (51105) hydrogen bonds : bond 0.03646 ( 1623) hydrogen bonds : angle 4.61296 ( 4514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11230.55 seconds wall clock time: 192 minutes 31.59 seconds (11551.59 seconds total)