Starting phenix.real_space_refine on Mon Oct 26 16:03:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s5z_24844/10_2026/7s5z_24844.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5z_24844/10_2026/7s5z_24844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s5z_24844/10_2026/7s5z_24844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5z_24844/10_2026/7s5z_24844.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s5z_24844/10_2026/7s5z_24844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5z_24844/10_2026/7s5z_24844.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s5z_24844/10_2026/7s5z_24844.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s5z_24844/10_2026/7s5z_24844.cif" } resolution = 3.9 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= -0.005 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 121 5.16 5 C 13673 2.51 5 N 3597 2.21 5 O 3750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21148 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "E" Number of atoms: 11012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1403, 11012 Classifications: {'peptide': 1403} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 42, 'TRANS': 1360} Chain breaks: 7 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Time building chain proxies: 4.77, per 1000 atoms: 0.23 Number of scatterers: 21148 At special positions: 0 Unit cell: (130, 154.7, 141.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 121 16.00 P 5 15.00 Mg 2 11.99 O 3750 8.00 N 3597 7.00 C 13673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 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: 1.62 Conformation dependent library (CDL) restraints added in 994.9 milliseconds 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 31 sheets defined 51.9% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 58 through 65 removed outlier: 4.131A pdb=" N THR A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 173 Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.527A pdb=" N LEU A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 330 through 333 Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.794A pdb=" N ASP A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 58 through 65 removed outlier: 4.132A pdb=" N THR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 142 through 173 Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.528A pdb=" N LEU B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.794A pdb=" N ASP B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 58 through 65 removed outlier: 4.131A pdb=" N THR C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 142 through 173 Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.528A pdb=" N LEU C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.793A pdb=" N ASP C 350 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 58 through 65 removed outlier: 4.131A pdb=" N THR D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 142 through 173 Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.527A pdb=" N LEU D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 345 through 350 removed outlier: 3.793A pdb=" N ASP D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 17 removed outlier: 3.617A pdb=" N ARG E 17 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 52 removed outlier: 3.563A pdb=" N VAL E 35 " --> pdb=" O ALA E 31 " (cutoff:3.500A) Proline residue: E 36 - end of helix Proline residue: E 46 - end of helix removed outlier: 3.526A pdb=" N TRP E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 97 removed outlier: 3.648A pdb=" N ASP E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 131 Processing helix chain 'E' and resid 137 through 162 Processing helix chain 'E' and resid 167 through 193 removed outlier: 3.697A pdb=" N CYS E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 231 Processing helix chain 'E' and resid 233 through 240 removed outlier: 4.214A pdb=" N PHE E 237 " --> pdb=" O TRP E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 275 removed outlier: 5.837A pdb=" N LEU E 267 " --> pdb=" O ASN E 263 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 310 removed outlier: 5.631A pdb=" N ARG E 298 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 328 Processing helix chain 'E' and resid 348 through 355 Processing helix chain 'E' and resid 355 through 402 removed outlier: 3.796A pdb=" N LEU E 359 " --> pdb=" O ASN E 355 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR E 394 " --> pdb=" O GLY E 390 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS E 402 " --> pdb=" O ASN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.154A pdb=" N LEU E 408 " --> pdb=" O SER E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 435 removed outlier: 5.293A pdb=" N ASN E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 456 removed outlier: 3.629A pdb=" N LEU E 439 " --> pdb=" O LEU E 435 " (cutoff:3.500A) Proline residue: E 443 - end of helix removed outlier: 3.600A pdb=" N ILE E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 506 removed outlier: 3.617A pdb=" N ILE E 463 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL E 467 " --> pdb=" O ILE E 463 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE E 469 " --> pdb=" O ALA E 465 " (cutoff:3.500A) Proline residue: E 473 - end of helix removed outlier: 3.636A pdb=" N TYR E 476 " --> pdb=" O ALA E 472 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU E 491 " --> pdb=" O ARG E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 513 Processing helix chain 'E' and resid 515 through 549 removed outlier: 3.530A pdb=" N SER E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 565 Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.623A pdb=" N ALA E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 616 Processing helix chain 'E' and resid 719 through 728 removed outlier: 3.620A pdb=" N LEU E 724 " --> pdb=" O LYS E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 790 Processing helix chain 'E' and resid 795 through 806 Processing helix chain 'E' and resid 808 through 815 Processing helix chain 'E' and resid 817 through 821 removed outlier: 3.666A pdb=" N GLN E 820 " --> pdb=" O HIS E 817 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR E 821 " --> pdb=" O GLY E 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 817 through 821' Processing helix chain 'E' and resid 832 through 845 Processing helix chain 'E' and resid 861 through 871 Processing helix chain 'E' and resid 890 through 897 removed outlier: 3.696A pdb=" N TYR E 893 " --> pdb=" O LYS E 890 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 894 " --> pdb=" O LEU E 891 " (cutoff:3.500A) Proline residue: E 895 - end of helix No H-bonds generated for 'chain 'E' and resid 890 through 897' Processing helix chain 'E' and resid 913 through 920 Processing helix chain 'E' and resid 921 through 933 Processing helix chain 'E' and resid 998 through 1009 removed outlier: 4.096A pdb=" N ALA E1002 " --> pdb=" O TRP E 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1038 Processing helix chain 'E' and resid 1066 through 1098 removed outlier: 3.666A pdb=" N VAL E1070 " --> pdb=" O MET E1066 " (cutoff:3.500A) Processing helix chain 'E' and resid 1100 through 1107 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.676A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1135 removed outlier: 3.563A pdb=" N ILE E1121 " --> pdb=" O PRO E1117 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 removed outlier: 3.544A pdb=" N SER E1146 " --> pdb=" O CYS E1142 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU E1148 " --> pdb=" O SER E1144 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E1149 " --> pdb=" O ARG E1145 " (cutoff:3.500A) Processing helix chain 'E' and resid 1164 through 1210 Proline residue: E1170 - end of helix removed outlier: 4.470A pdb=" N VAL E1184 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 3.568A pdb=" N GLU E1209 " --> pdb=" O ALA E1205 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E1210 " --> pdb=" O GLU E1206 " (cutoff:3.500A) Processing helix chain 'E' and resid 1210 through 1217 Processing helix chain 'E' and resid 1219 through 1273 removed outlier: 3.613A pdb=" N PHE E1223 " --> pdb=" O TYR E1219 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL E1260 " --> pdb=" O GLY E1256 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS E1273 " --> pdb=" O SER E1269 " (cutoff:3.500A) Processing helix chain 'E' and resid 1279 through 1320 removed outlier: 5.342A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS E1320 " --> pdb=" O HIS E1316 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1393 removed outlier: 3.859A pdb=" N SER E1389 " --> pdb=" O LYS E1385 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1421 Processing helix chain 'E' and resid 1436 through 1441 Processing helix chain 'E' and resid 1447 through 1457 Processing helix chain 'E' and resid 1460 through 1467 Processing helix chain 'E' and resid 1483 through 1498 removed outlier: 4.137A pdb=" N ARG E1498 " --> pdb=" O ARG E1494 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1524 Processing helix chain 'E' and resid 1539 through 1544 removed outlier: 3.913A pdb=" N ILE E1543 " --> pdb=" O ARG E1539 " (cutoff:3.500A) Processing helix chain 'E' and resid 1562 through 1568 Processing helix chain 'E' and resid 1572 through 1582 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL A 202 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 255 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 removed outlier: 4.395A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 221 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR A 223 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 322 Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.577A pdb=" N HIS E 60 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL B 202 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 255 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 210 through 211 removed outlier: 4.395A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 221 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR B 223 " --> pdb=" O PRO B 232 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 210 through 211 Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB4, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AB5, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL C 202 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 255 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'C' and resid 210 through 211 removed outlier: 4.395A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 210 through 211 Processing sheet with id=AB9, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AC1, first strand: chain 'C' and resid 319 through 322 Processing sheet with id=AC2, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 255 " --> pdb=" O VAL D 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'D' and resid 210 through 211 removed outlier: 4.395A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG D 221 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 210 through 211 Processing sheet with id=AC6, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AC7, first strand: chain 'D' and resid 319 through 322 Processing sheet with id=AC8, first strand: chain 'E' and resid 678 through 680 removed outlier: 7.167A pdb=" N ILE E 704 " --> pdb=" O CYS E 679 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 697 through 700 removed outlier: 3.598A pdb=" N ASN E 699 " --> pdb=" O GLY E 685 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLY E 685 " --> pdb=" O ASN E 699 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY E 684 " --> pdb=" O GLY E 736 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY E 736 " --> pdb=" O GLY E 684 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR E 686 " --> pdb=" O VAL E 734 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN E 732 " --> pdb=" O THR E 688 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 850 through 853 removed outlier: 6.309A pdb=" N THR E 710 " --> pdb=" O LEU E 886 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 1365 through 1369 removed outlier: 5.368A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER E1351 " --> pdb=" O PHE E1399 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE E1399 " --> pdb=" O SER E1351 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 1424 through 1425 removed outlier: 3.528A pdb=" N VAL E1551 " --> pdb=" O GLU E1559 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 1434 through 1435 1164 hydrogen bonds defined for protein. 3384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6588 1.34 - 1.46: 4241 1.46 - 1.58: 10580 1.58 - 1.70: 8 1.70 - 1.81: 194 Bond restraints: 21611 Sorted by residual: bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.98e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.87e+01 bond pdb=" C ILE E1136 " pdb=" N PRO E1137 " ideal model delta sigma weight residual 1.336 1.403 -0.067 1.20e-02 6.94e+03 3.09e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.325 0.049 1.00e-02 1.00e+04 2.42e+01 bond pdb=" C5 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.31e+01 ... (remaining 21606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 29106 3.77 - 7.54: 218 7.54 - 11.30: 36 11.30 - 15.07: 3 15.07 - 18.84: 2 Bond angle restraints: 29365 Sorted by residual: angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 117.99 18.84 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 125.45 14.42 1.00e+00 1.00e+00 2.08e+02 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 119.32 7.48 1.00e+00 1.00e+00 5.59e+01 angle pdb=" N3 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 127.04 134.77 -7.73 1.15e+00 7.59e-01 4.54e+01 angle pdb=" C ASN E 263 " pdb=" N TYR E 264 " pdb=" CA TYR E 264 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.84e+01 ... (remaining 29360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.38: 11939 26.38 - 52.75: 757 52.75 - 79.13: 111 79.13 - 105.50: 6 105.50 - 131.88: 1 Dihedral angle restraints: 12814 sinusoidal: 5011 harmonic: 7803 Sorted by residual: dihedral pdb=" CA ILE E 61 " pdb=" C ILE E 61 " pdb=" N HIS E 62 " pdb=" CA HIS E 62 " ideal model delta harmonic sigma weight residual 180.00 141.72 38.28 0 5.00e+00 4.00e-02 5.86e+01 dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 142 " pdb=" CB CYS B 142 " ideal model delta sinusoidal sigma weight residual 93.00 29.23 63.77 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CB CYS C 110 " pdb=" SG CYS C 110 " pdb=" SG CYS C 142 " pdb=" CB CYS C 142 " ideal model delta sinusoidal sigma weight residual 93.00 29.25 63.75 1 1.00e+01 1.00e-02 5.35e+01 ... (remaining 12811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2639 0.062 - 0.124: 717 0.124 - 0.186: 97 0.186 - 0.249: 18 0.249 - 0.311: 3 Chirality restraints: 3474 Sorted by residual: chirality pdb=" CB ILE E 712 " pdb=" CA ILE E 712 " pdb=" CG1 ILE E 712 " pdb=" CG2 ILE E 712 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB ILE E 704 " pdb=" CA ILE E 704 " pdb=" CG1 ILE E 704 " pdb=" CG2 ILE E 704 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL E1396 " pdb=" CA VAL E1396 " pdb=" CG1 VAL E1396 " pdb=" CG2 VAL E1396 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3471 not shown) Planarity restraints: 3650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 264 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C TYR E 264 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR E 264 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN E 265 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 261 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C LEU E 261 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU E 261 " -0.023 2.00e-02 2.50e+03 pdb=" N THR E 262 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 422 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C VAL E 422 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL E 422 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA E 423 " 0.016 2.00e-02 2.50e+03 ... (remaining 3647 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 337 2.64 - 3.20: 19064 3.20 - 3.77: 35650 3.77 - 4.33: 45499 4.33 - 4.90: 73763 Nonbonded interactions: 174313 Sorted by model distance: nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.073 2.170 nonbonded pdb="MG MG E1602 " pdb=" O3A ATP E1604 " model vdw 2.085 2.170 nonbonded pdb=" OG SER E 721 " pdb="MG MG E1602 " model vdw 2.088 2.170 nonbonded pdb=" O1B ADP E1601 " pdb="MG MG E1603 " model vdw 2.118 2.170 nonbonded pdb=" NE2 GLN E 775 " pdb="MG MG E1602 " model vdw 2.169 2.250 ... (remaining 174308 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.780 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 0.077 21615 Z= 0.279 Angle : 0.961 18.839 29373 Z= 0.544 Chirality : 0.056 0.311 3474 Planarity : 0.007 0.069 3650 Dihedral : 16.761 131.879 7732 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 6.47 % Allowed : 8.33 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.13), residues: 2663 helix: -2.12 (0.10), residues: 1327 sheet: -2.27 (0.26), residues: 274 loop : -2.02 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1421 TYR 0.023 0.002 TYR E 264 PHE 0.021 0.002 PHE E 578 TRP 0.015 0.002 TRP E 289 HIS 0.010 0.001 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.28 (21611) covalent geometry : angle 0.96026 / 0.54 (29365) SS BOND : bond 0.00101 / 0.05 ( 4) SS BOND : angle 2.49702 / 1.46 ( 8) hydrogen bonds : bond 0.15788 / 10.53 ( 1148) hydrogen bonds : angle 6.74386 / 4.72 ( 3384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 532 time to evaluate : 0.796 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: symmetry clash REVERT: A 39 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8693 (ttmt) REVERT: A 51 GLU cc_start: 0.8213 (tp30) cc_final: 0.7682 (tp30) REVERT: A 57 GLN cc_start: 0.8338 (tt0) cc_final: 0.7845 (tp40) REVERT: A 66 LEU cc_start: 0.9172 (mt) cc_final: 0.8878 (mt) REVERT: A 73 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8752 (tt) REVERT: A 163 MET cc_start: 0.9476 (mmm) cc_final: 0.9264 (mmm) REVERT: A 170 LYS cc_start: 0.9416 (tptp) cc_final: 0.9156 (tptt) REVERT: A 237 ASP cc_start: 0.7721 (p0) cc_final: 0.7181 (p0) REVERT: A 330 TYR cc_start: 0.8745 (m-80) cc_final: 0.8440 (m-80) REVERT: B 80 LEU cc_start: 0.9657 (mm) cc_final: 0.9441 (mp) REVERT: B 84 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8862 (mt) REVERT: B 160 ASN cc_start: 0.9148 (m110) cc_final: 0.8900 (m110) REVERT: B 163 MET cc_start: 0.9505 (mmm) cc_final: 0.9099 (mmm) REVERT: B 169 MET cc_start: 0.8818 (ttm) cc_final: 0.8606 (ttm) REVERT: B 176 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7204 (mtp180) REVERT: B 179 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8415 (mt-10) REVERT: B 181 LEU cc_start: 0.9532 (mt) cc_final: 0.9307 (mt) REVERT: B 202 VAL cc_start: 0.9676 (OUTLIER) cc_final: 0.9446 (p) REVERT: B 220 VAL cc_start: 0.9573 (OUTLIER) cc_final: 0.9355 (p) REVERT: B 231 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8171 (m) REVERT: B 240 MET cc_start: 0.9075 (tmm) cc_final: 0.8763 (tmm) REVERT: B 302 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.9026 (m) REVERT: B 305 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8633 (mm) REVERT: C 39 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8799 (tmtt) REVERT: C 41 ASN cc_start: 0.9011 (m110) cc_final: 0.8774 (m110) REVERT: C 48 ASN cc_start: 0.8817 (m-40) cc_final: 0.7524 (m-40) REVERT: C 56 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9055 (mt) REVERT: C 65 ASP cc_start: 0.8387 (t0) cc_final: 0.8072 (t0) REVERT: C 91 TRP cc_start: 0.9271 (t60) cc_final: 0.9024 (t60) REVERT: C 128 GLN cc_start: 0.9013 (tt0) cc_final: 0.8756 (tt0) REVERT: C 160 ASN cc_start: 0.9078 (m110) cc_final: 0.8524 (m110) REVERT: C 163 MET cc_start: 0.9272 (mmm) cc_final: 0.9052 (mmt) REVERT: C 169 MET cc_start: 0.8991 (ttm) cc_final: 0.8696 (ttm) REVERT: C 240 MET cc_start: 0.9158 (tmm) cc_final: 0.8645 (tmm) REVERT: C 279 GLN cc_start: 0.8925 (tp40) cc_final: 0.8116 (tm-30) REVERT: D 54 ARG cc_start: 0.8478 (ptp-110) cc_final: 0.8161 (ptm160) REVERT: D 64 VAL cc_start: 0.9748 (OUTLIER) cc_final: 0.9525 (t) REVERT: D 65 ASP cc_start: 0.9010 (t0) cc_final: 0.8610 (t70) REVERT: D 77 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8434 (tpp) REVERT: D 163 MET cc_start: 0.9109 (mmm) cc_final: 0.8690 (mmm) REVERT: D 170 LYS cc_start: 0.9073 (tptp) cc_final: 0.8467 (tptt) REVERT: D 262 ASP cc_start: 0.9206 (t0) cc_final: 0.8875 (t70) REVERT: D 265 SER cc_start: 0.9077 (m) cc_final: 0.8767 (p) REVERT: D 330 TYR cc_start: 0.8019 (m-80) cc_final: 0.7720 (m-80) REVERT: E 30 ASP cc_start: 0.8793 (m-30) cc_final: 0.8540 (m-30) REVERT: E 116 MET cc_start: 0.9423 (mmm) cc_final: 0.9109 (mmm) REVERT: E 153 ILE cc_start: 0.9491 (mm) cc_final: 0.9185 (mm) REVERT: E 508 LYS cc_start: 0.9468 (tttt) cc_final: 0.9219 (ttmm) REVERT: E 547 MET cc_start: 0.9015 (tmm) cc_final: 0.8793 (tmm) REVERT: E 584 PHE cc_start: 0.9021 (m-80) cc_final: 0.8736 (m-80) REVERT: E 591 LEU cc_start: 0.9330 (tp) cc_final: 0.8975 (tp) REVERT: E 1020 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8816 (tt0) REVERT: E 1034 LEU cc_start: 0.9347 (tp) cc_final: 0.9133 (tt) REVERT: E 1188 ASP cc_start: 0.8659 (t70) cc_final: 0.8424 (t0) REVERT: E 1191 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8700 (tp-100) REVERT: E 1229 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7872 (mp0) REVERT: E 1290 MET cc_start: 0.8962 (tpp) cc_final: 0.8343 (mmp) REVERT: E 1305 MET cc_start: 0.9338 (tpt) cc_final: 0.9102 (tpp) REVERT: E 1496 PHE cc_start: 0.8604 (m-10) cc_final: 0.8308 (m-80) outliers start: 149 outliers final: 35 residues processed: 625 average time/residue: 0.1467 time to fit residues: 143.0124 Evaluate side-chains 395 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 347 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 770 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 HIS B 279 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 175 HIS C 277 HIS C 278 HIS ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS E 106 HIS E 167 GLN E 407 ASN E 438 ASN E 499 GLN E 715 GLN E 923 GLN E 933 ASN ** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1308 GLN E1348 GLN E1364 HIS E1439 ASN E1486 GLN E1488 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.064614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.053717 restraints weight = 91680.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.055408 restraints weight = 45516.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.056556 restraints weight = 28237.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.057349 restraints weight = 20164.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.057750 restraints weight = 15805.796| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21615 Z= 0.168 Angle : 0.654 11.784 29373 Z= 0.343 Chirality : 0.044 0.234 3474 Planarity : 0.005 0.059 3650 Dihedral : 7.154 111.131 2948 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.26 % Allowed : 17.36 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.15), residues: 2663 helix: -0.34 (0.13), residues: 1362 sheet: -1.41 (0.31), residues: 242 loop : -1.77 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 835 TYR 0.013 0.001 TYR E 379 PHE 0.026 0.002 PHE E1503 TRP 0.015 0.001 TRP A 311 HIS 0.005 0.001 HIS E 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (21611) covalent geometry : angle 0.65325 / 0.34 (29365) SS BOND : bond 0.00368 / 0.18 ( 4) SS BOND : angle 2.38410 / 1.42 ( 8) hydrogen bonds : bond 0.04470 / 2.97 ( 1148) hydrogen bonds : angle 4.72230 / 3.32 ( 3384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 375 time to evaluate : 0.820 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 59 VAL cc_start: 0.9307 (m) cc_final: 0.9008 (t) REVERT: A 66 LEU cc_start: 0.9078 (mt) cc_final: 0.8772 (mt) REVERT: A 83 TRP cc_start: 0.9564 (m-10) cc_final: 0.8967 (m-90) REVERT: A 141 GLU cc_start: 0.8760 (tp30) cc_final: 0.8352 (tp30) REVERT: A 163 MET cc_start: 0.9563 (mmm) cc_final: 0.9239 (mmm) REVERT: A 170 LYS cc_start: 0.9502 (tptp) cc_final: 0.9079 (tptt) REVERT: A 268 TYR cc_start: 0.9018 (t80) cc_final: 0.8751 (t80) REVERT: A 330 TYR cc_start: 0.8743 (m-80) cc_final: 0.8531 (m-80) REVERT: B 80 LEU cc_start: 0.9680 (mm) cc_final: 0.9468 (mp) REVERT: B 160 ASN cc_start: 0.9197 (m-40) cc_final: 0.8914 (m-40) REVERT: B 179 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: B 185 LYS cc_start: 0.9203 (ttmm) cc_final: 0.8598 (tptp) REVERT: B 231 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8867 (m) REVERT: B 240 MET cc_start: 0.9294 (tmm) cc_final: 0.8730 (tmm) REVERT: B 296 ILE cc_start: 0.9217 (mp) cc_final: 0.8943 (tt) REVERT: B 330 TYR cc_start: 0.8618 (m-80) cc_final: 0.7890 (m-80) REVERT: C 39 LYS cc_start: 0.9308 (mmmm) cc_final: 0.8759 (tmtt) REVERT: C 47 LYS cc_start: 0.8269 (tppt) cc_final: 0.7897 (tppt) REVERT: C 63 LEU cc_start: 0.9636 (tp) cc_final: 0.9327 (tt) REVERT: C 65 ASP cc_start: 0.8400 (t0) cc_final: 0.8056 (t0) REVERT: C 84 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9007 (tt) REVERT: C 160 ASN cc_start: 0.9208 (m-40) cc_final: 0.8774 (m110) REVERT: C 169 MET cc_start: 0.8971 (ttm) cc_final: 0.8709 (ttm) REVERT: C 170 LYS cc_start: 0.9441 (tptm) cc_final: 0.9204 (tttp) REVERT: C 179 GLU cc_start: 0.8530 (mp0) cc_final: 0.8069 (mp0) REVERT: C 185 LYS cc_start: 0.9372 (mmtm) cc_final: 0.9046 (mmtm) REVERT: C 214 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.8656 (t) REVERT: C 240 MET cc_start: 0.8574 (tmm) cc_final: 0.8202 (tmm) REVERT: C 247 ASN cc_start: 0.8717 (p0) cc_final: 0.8340 (p0) REVERT: C 279 GLN cc_start: 0.8986 (tp40) cc_final: 0.8137 (tm-30) REVERT: D 65 ASP cc_start: 0.8975 (t0) cc_final: 0.8621 (t70) REVERT: D 77 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8297 (tpp) REVERT: D 163 MET cc_start: 0.9187 (mmm) cc_final: 0.8809 (mmm) REVERT: D 170 LYS cc_start: 0.9149 (tptp) cc_final: 0.8540 (tptm) REVERT: D 179 GLU cc_start: 0.8146 (tp30) cc_final: 0.7892 (tp30) REVERT: D 262 ASP cc_start: 0.9152 (t0) cc_final: 0.8899 (t70) REVERT: D 293 THR cc_start: 0.9315 (p) cc_final: 0.8959 (p) REVERT: D 335 ASN cc_start: 0.8596 (t0) cc_final: 0.8378 (t0) REVERT: E 30 ASP cc_start: 0.8794 (m-30) cc_final: 0.8465 (m-30) REVERT: E 153 ILE cc_start: 0.9507 (mm) cc_final: 0.9241 (mm) REVERT: E 442 MET cc_start: 0.8748 (tpt) cc_final: 0.8501 (tpt) REVERT: E 508 LYS cc_start: 0.9523 (tttt) cc_final: 0.9303 (ttmm) REVERT: E 547 MET cc_start: 0.8771 (tmm) cc_final: 0.8455 (tmm) REVERT: E 584 PHE cc_start: 0.8951 (m-80) cc_final: 0.8695 (m-80) REVERT: E 790 PHE cc_start: 0.8649 (t80) cc_final: 0.8408 (t80) REVERT: E 1188 ASP cc_start: 0.8579 (t70) cc_final: 0.8156 (t0) REVERT: E 1191 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8710 (tp-100) REVERT: E 1290 MET cc_start: 0.8962 (tpp) cc_final: 0.8614 (mmp) REVERT: E 1305 MET cc_start: 0.9399 (tpt) cc_final: 0.9183 (tpp) REVERT: E 1395 MET cc_start: 0.8750 (mmm) cc_final: 0.8534 (mmm) REVERT: E 1402 HIS cc_start: 0.8225 (m-70) cc_final: 0.7439 (t-170) REVERT: E 1404 ILE cc_start: 0.9065 (mt) cc_final: 0.8626 (pt) outliers start: 75 outliers final: 41 residues processed: 431 average time/residue: 0.1345 time to fit residues: 93.5632 Evaluate side-chains 354 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 308 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1198 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1362 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [264, 132, 106, 148, 85, 59, 30, 20, 171, 38, 267] chunk 264 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 173 GLN C 279 GLN D 48 ASN D 128 GLN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 475 GLN ** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.065190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.054447 restraints weight = 91852.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.056122 restraints weight = 45812.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.057255 restraints weight = 28410.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.058031 restraints weight = 20267.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.058501 restraints weight = 15886.175| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21615 Z= 0.138 Angle : 0.612 11.720 29373 Z= 0.314 Chirality : 0.043 0.206 3474 Planarity : 0.004 0.065 3650 Dihedral : 6.106 88.129 2898 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.30 % Allowed : 19.66 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.16), residues: 2663 helix: 0.35 (0.14), residues: 1361 sheet: -0.68 (0.31), residues: 254 loop : -1.60 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1579 TYR 0.015 0.001 TYR E1287 PHE 0.030 0.001 PHE E1496 TRP 0.018 0.001 TRP A 311 HIS 0.007 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (21611) covalent geometry : angle 0.61109 / 0.31 (29365) SS BOND : bond 0.00241 / 0.12 ( 4) SS BOND : angle 1.99775 / 1.21 ( 8) hydrogen bonds : bond 0.04095 / 2.70 ( 1148) hydrogen bonds : angle 4.42385 / 3.11 ( 3384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 349 time to evaluate : 0.603 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: A 56 LEU cc_start: 0.9053 (mt) cc_final: 0.8767 (pp) REVERT: A 59 VAL cc_start: 0.9320 (m) cc_final: 0.9023 (t) REVERT: A 83 TRP cc_start: 0.9564 (m-10) cc_final: 0.8988 (m-90) REVERT: A 163 MET cc_start: 0.9541 (mmm) cc_final: 0.9225 (mmm) REVERT: A 268 TYR cc_start: 0.9055 (t80) cc_final: 0.8808 (t80) REVERT: A 292 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8118 (tm-30) REVERT: A 332 LYS cc_start: 0.9393 (pttt) cc_final: 0.9105 (ptpp) REVERT: B 160 ASN cc_start: 0.9105 (m-40) cc_final: 0.8832 (m110) REVERT: B 169 MET cc_start: 0.9009 (ttm) cc_final: 0.8770 (ttm) REVERT: B 179 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8456 (mt-10) REVERT: B 185 LYS cc_start: 0.9295 (ttmm) cc_final: 0.8899 (tptt) REVERT: B 231 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8858 (m) REVERT: B 240 MET cc_start: 0.9239 (tmm) cc_final: 0.8495 (tmm) REVERT: C 39 LYS cc_start: 0.9291 (mmmm) cc_final: 0.8685 (tmtt) REVERT: C 47 LYS cc_start: 0.8287 (tppt) cc_final: 0.7965 (tppt) REVERT: C 63 LEU cc_start: 0.9617 (tp) cc_final: 0.9390 (tt) REVERT: C 65 ASP cc_start: 0.8343 (t0) cc_final: 0.7987 (t0) REVERT: C 84 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8911 (tt) REVERT: C 160 ASN cc_start: 0.9197 (m-40) cc_final: 0.8767 (m110) REVERT: C 169 MET cc_start: 0.9025 (ttm) cc_final: 0.8699 (ttm) REVERT: C 170 LYS cc_start: 0.9464 (tptm) cc_final: 0.9110 (tttp) REVERT: C 179 GLU cc_start: 0.8593 (mp0) cc_final: 0.7987 (mp0) REVERT: C 214 THR cc_start: 0.9364 (OUTLIER) cc_final: 0.8084 (t) REVERT: C 247 ASN cc_start: 0.8708 (p0) cc_final: 0.8225 (p0) REVERT: C 332 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9024 (pttp) REVERT: C 349 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9189 (mm) REVERT: D 55 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8638 (t80) REVERT: D 65 ASP cc_start: 0.8985 (t0) cc_final: 0.8631 (t70) REVERT: D 88 MET cc_start: 0.8450 (tmm) cc_final: 0.7893 (tmm) REVERT: D 163 MET cc_start: 0.9142 (mmm) cc_final: 0.8727 (mmm) REVERT: D 170 LYS cc_start: 0.9159 (tptp) cc_final: 0.8599 (tptm) REVERT: D 179 GLU cc_start: 0.8109 (tp30) cc_final: 0.7649 (tp30) REVERT: D 262 ASP cc_start: 0.9071 (t0) cc_final: 0.8769 (t70) REVERT: D 335 ASN cc_start: 0.8558 (t0) cc_final: 0.8211 (t0) REVERT: E 30 ASP cc_start: 0.8826 (m-30) cc_final: 0.8550 (m-30) REVERT: E 83 LEU cc_start: 0.9514 (mt) cc_final: 0.9289 (mt) REVERT: E 108 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: E 153 ILE cc_start: 0.9500 (mm) cc_final: 0.9183 (mm) REVERT: E 311 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8505 (p0) REVERT: E 419 CYS cc_start: 0.9220 (m) cc_final: 0.8948 (t) REVERT: E 442 MET cc_start: 0.8793 (tpt) cc_final: 0.8588 (tpt) REVERT: E 508 LYS cc_start: 0.9494 (tttt) cc_final: 0.9233 (ttmm) REVERT: E 584 PHE cc_start: 0.8922 (m-80) cc_final: 0.8621 (m-80) REVERT: E 790 PHE cc_start: 0.8616 (t80) cc_final: 0.8332 (t80) REVERT: E 1080 LEU cc_start: 0.9287 (tp) cc_final: 0.8993 (mt) REVERT: E 1143 LEU cc_start: 0.9642 (tp) cc_final: 0.9227 (pp) REVERT: E 1188 ASP cc_start: 0.8624 (t70) cc_final: 0.8317 (t0) REVERT: E 1191 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8711 (tp-100) REVERT: E 1232 ASP cc_start: 0.8766 (m-30) cc_final: 0.8564 (m-30) REVERT: E 1290 MET cc_start: 0.8923 (tpp) cc_final: 0.8587 (mmp) REVERT: E 1395 MET cc_start: 0.8837 (mmm) cc_final: 0.8622 (mmm) REVERT: E 1402 HIS cc_start: 0.8154 (m-70) cc_final: 0.7876 (t-170) REVERT: E 1505 MET cc_start: 0.8655 (mpp) cc_final: 0.7976 (mpp) outliers start: 76 outliers final: 44 residues processed: 404 average time/residue: 0.1295 time to fit residues: 85.1150 Evaluate side-chains 367 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 315 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1239 LEU Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1362 LEU Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [238, 67, 259, 201, 266, 171, 74, 168, 183, 51, 54] chunk 238 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 51 optimal weight: 0.0020 chunk 54 optimal weight: 0.9980 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 889 HIS ** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.053143 restraints weight = 92693.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.054823 restraints weight = 46425.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.055954 restraints weight = 28886.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.056719 restraints weight = 20718.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.057246 restraints weight = 16349.230| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21615 Z= 0.190 Angle : 0.635 11.197 29373 Z= 0.325 Chirality : 0.043 0.174 3474 Planarity : 0.004 0.062 3650 Dihedral : 5.781 94.591 2890 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.21 % Allowed : 20.62 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2663 helix: 0.70 (0.14), residues: 1361 sheet: -0.62 (0.31), residues: 254 loop : -1.43 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1579 TYR 0.015 0.001 TYR E1287 PHE 0.026 0.002 PHE E1496 TRP 0.015 0.001 TRP B 83 HIS 0.005 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (21611) covalent geometry : angle 0.63433 / 0.32 (29365) SS BOND : bond 0.00255 / 0.13 ( 4) SS BOND : angle 2.07410 / 1.31 ( 8) hydrogen bonds : bond 0.04149 / 2.72 ( 1148) hydrogen bonds : angle 4.36541 / 3.08 ( 3384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 320 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9281 (mt) cc_final: 0.8915 (pp) REVERT: A 163 MET cc_start: 0.9595 (mmm) cc_final: 0.9337 (mmm) REVERT: A 170 LYS cc_start: 0.9518 (tptp) cc_final: 0.9302 (tptm) REVERT: A 292 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8132 (tm-30) REVERT: A 332 LYS cc_start: 0.9425 (pttt) cc_final: 0.9077 (ptpp) REVERT: B 160 ASN cc_start: 0.9084 (m-40) cc_final: 0.8822 (m-40) REVERT: B 169 MET cc_start: 0.9048 (ttm) cc_final: 0.8813 (ttm) REVERT: B 185 LYS cc_start: 0.9348 (ttmm) cc_final: 0.8941 (tptm) REVERT: B 231 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8871 (m) REVERT: B 240 MET cc_start: 0.9198 (tmm) cc_final: 0.8437 (tmm) REVERT: B 296 ILE cc_start: 0.9303 (mp) cc_final: 0.8882 (tt) REVERT: C 39 LYS cc_start: 0.9313 (mmmm) cc_final: 0.8783 (tmtt) REVERT: C 47 LYS cc_start: 0.8319 (tppt) cc_final: 0.8067 (tppt) REVERT: C 65 ASP cc_start: 0.8510 (t0) cc_final: 0.8077 (t0) REVERT: C 84 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9060 (tt) REVERT: C 169 MET cc_start: 0.9018 (ttm) cc_final: 0.8694 (ttm) REVERT: C 170 LYS cc_start: 0.9497 (tptm) cc_final: 0.9274 (tttm) REVERT: C 179 GLU cc_start: 0.8602 (mp0) cc_final: 0.8014 (mp0) REVERT: C 214 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.8843 (t) REVERT: C 240 MET cc_start: 0.7880 (tmm) cc_final: 0.7011 (tmm) REVERT: C 332 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8951 (pttp) REVERT: D 55 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8673 (t80) REVERT: D 56 LEU cc_start: 0.9298 (tp) cc_final: 0.8983 (tt) REVERT: D 65 ASP cc_start: 0.8952 (t0) cc_final: 0.8688 (t70) REVERT: D 88 MET cc_start: 0.8593 (tmm) cc_final: 0.7916 (tmm) REVERT: D 163 MET cc_start: 0.9277 (mmm) cc_final: 0.8881 (mmm) REVERT: D 170 LYS cc_start: 0.9281 (tptp) cc_final: 0.8690 (tptt) REVERT: D 179 GLU cc_start: 0.8304 (tp30) cc_final: 0.7876 (tp30) REVERT: D 262 ASP cc_start: 0.9030 (t0) cc_final: 0.8709 (t70) REVERT: E 30 ASP cc_start: 0.8827 (m-30) cc_final: 0.8541 (m-30) REVERT: E 73 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8886 (p0) REVERT: E 83 LEU cc_start: 0.9591 (mt) cc_final: 0.9376 (mt) REVERT: E 108 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: E 153 ILE cc_start: 0.9526 (mm) cc_final: 0.9207 (mm) REVERT: E 226 LEU cc_start: 0.8746 (tt) cc_final: 0.8522 (tp) REVERT: E 315 PHE cc_start: 0.8487 (m-80) cc_final: 0.8285 (m-80) REVERT: E 442 MET cc_start: 0.8827 (tpt) cc_final: 0.8563 (tpt) REVERT: E 451 ILE cc_start: 0.9408 (mm) cc_final: 0.9156 (tp) REVERT: E 503 MET cc_start: 0.9298 (tpt) cc_final: 0.9017 (tpt) REVERT: E 611 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9409 (mm) REVERT: E 790 PHE cc_start: 0.8640 (t80) cc_final: 0.8385 (t80) REVERT: E 1110 MET cc_start: 0.8589 (mtp) cc_final: 0.8284 (mmm) REVERT: E 1129 CYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8101 (p) REVERT: E 1143 LEU cc_start: 0.9602 (tp) cc_final: 0.9250 (pp) REVERT: E 1191 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8768 (tp-100) REVERT: E 1280 LEU cc_start: 0.9045 (mm) cc_final: 0.8665 (tp) REVERT: E 1402 HIS cc_start: 0.8130 (m-70) cc_final: 0.7929 (t-170) outliers start: 97 outliers final: 60 residues processed: 397 average time/residue: 0.1300 time to fit residues: 84.5302 Evaluate side-chains 366 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 297 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1239 LEU Chi-restraints excluded: chain E residue 1258 CYS Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1375 ILE Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [65, 183, 238, 134, 241, 190, 198, 250, 207, 54, 57] chunk 65 optimal weight: 9.9990 chunk 183 optimal weight: 0.0470 chunk 238 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054510 restraints weight = 91097.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.056203 restraints weight = 45266.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.057345 restraints weight = 28113.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.058125 restraints weight = 20034.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058606 restraints weight = 15728.156| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21615 Z= 0.131 Angle : 0.604 11.744 29373 Z= 0.305 Chirality : 0.043 0.177 3474 Planarity : 0.004 0.066 3650 Dihedral : 5.613 97.016 2888 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.12 % Allowed : 21.96 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.16), residues: 2663 helix: 0.73 (0.14), residues: 1384 sheet: -0.26 (0.32), residues: 246 loop : -1.40 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1579 TYR 0.027 0.001 TYR C 268 PHE 0.023 0.001 PHE E 364 TRP 0.019 0.001 TRP A 83 HIS 0.005 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (21611) covalent geometry : angle 0.60366 / 0.30 (29365) SS BOND : bond 0.00277 / 0.14 ( 4) SS BOND : angle 1.80829 / 1.15 ( 8) hydrogen bonds : bond 0.03923 / 2.58 ( 1148) hydrogen bonds : angle 4.24581 / 2.99 ( 3384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 339 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9270 (mt) cc_final: 0.8897 (pp) REVERT: A 83 TRP cc_start: 0.9692 (m-10) cc_final: 0.9076 (m-90) REVERT: A 163 MET cc_start: 0.9578 (mmm) cc_final: 0.9290 (mmm) REVERT: A 292 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 332 LYS cc_start: 0.9373 (pttt) cc_final: 0.9173 (ptpp) REVERT: B 47 LYS cc_start: 0.9264 (tppt) cc_final: 0.9059 (tppt) REVERT: B 148 ILE cc_start: 0.9683 (tt) cc_final: 0.9428 (tp) REVERT: B 160 ASN cc_start: 0.9083 (m-40) cc_final: 0.8821 (m-40) REVERT: B 169 MET cc_start: 0.8980 (ttm) cc_final: 0.8618 (ttm) REVERT: B 185 LYS cc_start: 0.9312 (ttmm) cc_final: 0.8928 (tptt) REVERT: B 231 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8849 (m) REVERT: B 240 MET cc_start: 0.9160 (tmm) cc_final: 0.8412 (tmm) REVERT: B 296 ILE cc_start: 0.9278 (mp) cc_final: 0.8856 (tt) REVERT: B 332 LYS cc_start: 0.9175 (mtmt) cc_final: 0.8969 (mtmm) REVERT: C 39 LYS cc_start: 0.9220 (mmmm) cc_final: 0.8707 (tmtt) REVERT: C 47 LYS cc_start: 0.8742 (tppt) cc_final: 0.8331 (tppt) REVERT: C 65 ASP cc_start: 0.8383 (t0) cc_final: 0.7999 (t0) REVERT: C 84 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9047 (tt) REVERT: C 160 ASN cc_start: 0.9180 (m-40) cc_final: 0.8793 (m110) REVERT: C 169 MET cc_start: 0.8990 (ttm) cc_final: 0.8642 (ttm) REVERT: C 170 LYS cc_start: 0.9488 (tptm) cc_final: 0.9204 (tttm) REVERT: C 179 GLU cc_start: 0.8573 (mp0) cc_final: 0.7951 (mp0) REVERT: C 214 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.8796 (t) REVERT: C 240 MET cc_start: 0.7917 (tmm) cc_final: 0.7135 (tmm) REVERT: C 262 ASP cc_start: 0.8718 (t0) cc_final: 0.8463 (t70) REVERT: C 332 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8938 (pttp) REVERT: D 55 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8678 (t80) REVERT: D 56 LEU cc_start: 0.9317 (tp) cc_final: 0.9004 (tt) REVERT: D 65 ASP cc_start: 0.8902 (t0) cc_final: 0.8697 (t70) REVERT: D 88 MET cc_start: 0.8596 (tmm) cc_final: 0.7879 (tmm) REVERT: D 128 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.9060 (tt0) REVERT: D 163 MET cc_start: 0.9267 (mmm) cc_final: 0.8895 (mmm) REVERT: D 170 LYS cc_start: 0.9232 (tptp) cc_final: 0.8632 (tptt) REVERT: D 179 GLU cc_start: 0.8131 (tp30) cc_final: 0.7785 (tp30) REVERT: D 262 ASP cc_start: 0.8970 (t0) cc_final: 0.8739 (t70) REVERT: E 10 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: E 30 ASP cc_start: 0.8823 (m-30) cc_final: 0.8597 (m-30) REVERT: E 80 PHE cc_start: 0.8605 (m-80) cc_final: 0.8271 (m-80) REVERT: E 108 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: E 153 ILE cc_start: 0.9526 (mm) cc_final: 0.9233 (mm) REVERT: E 226 LEU cc_start: 0.8704 (tt) cc_final: 0.8453 (tp) REVERT: E 419 CYS cc_start: 0.9318 (m) cc_final: 0.9059 (t) REVERT: E 503 MET cc_start: 0.9197 (tpt) cc_final: 0.8890 (tpt) REVERT: E 584 PHE cc_start: 0.8943 (m-80) cc_final: 0.8531 (m-80) REVERT: E 591 LEU cc_start: 0.9009 (tp) cc_final: 0.8763 (tp) REVERT: E 1080 LEU cc_start: 0.9310 (tp) cc_final: 0.9029 (mt) REVERT: E 1129 CYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8111 (p) REVERT: E 1143 LEU cc_start: 0.9618 (tp) cc_final: 0.9284 (pp) REVERT: E 1188 ASP cc_start: 0.8671 (t70) cc_final: 0.8334 (t0) REVERT: E 1280 LEU cc_start: 0.9098 (mm) cc_final: 0.8701 (tp) outliers start: 95 outliers final: 61 residues processed: 412 average time/residue: 0.1285 time to fit residues: 86.8090 Evaluate side-chains 376 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 306 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 775 GLN Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1239 LEU Chi-restraints excluded: chain E residue 1258 CYS Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1375 ILE Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [150, 106, 4, 27, 65, 21, 59, 209, 83, 124, 88] chunk 150 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 21 optimal weight: 0.3980 chunk 59 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN D 46 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN E 73 ASN E 161 HIS ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.065012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.053949 restraints weight = 92087.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.055641 restraints weight = 46130.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.056779 restraints weight = 28759.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.057562 restraints weight = 20541.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.058049 restraints weight = 16144.852| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21615 Z= 0.153 Angle : 0.622 11.512 29373 Z= 0.313 Chirality : 0.043 0.185 3474 Planarity : 0.004 0.062 3650 Dihedral : 5.578 100.046 2888 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.56 % Allowed : 22.74 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.16), residues: 2663 helix: 0.74 (0.14), residues: 1400 sheet: -0.31 (0.32), residues: 254 loop : -1.23 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1579 TYR 0.014 0.001 TYR C 268 PHE 0.030 0.001 PHE E 133 TRP 0.016 0.001 TRP B 83 HIS 0.005 0.001 HIS E1402 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (21611) covalent geometry : angle 0.62061 / 0.31 (29365) SS BOND : bond 0.00267 / 0.14 ( 4) SS BOND : angle 2.31789 / 1.42 ( 8) hydrogen bonds : bond 0.03924 / 2.58 ( 1148) hydrogen bonds : angle 4.22584 / 2.98 ( 3384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 320 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9329 (mt) cc_final: 0.8923 (pp) REVERT: A 83 TRP cc_start: 0.9668 (m-10) cc_final: 0.9098 (m-90) REVERT: A 163 MET cc_start: 0.9584 (mmm) cc_final: 0.9328 (mmm) REVERT: A 292 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8122 (tm-30) REVERT: B 148 ILE cc_start: 0.9691 (tt) cc_final: 0.9445 (tp) REVERT: B 160 ASN cc_start: 0.9091 (m-40) cc_final: 0.8793 (m110) REVERT: B 185 LYS cc_start: 0.9326 (ttmm) cc_final: 0.8917 (tptt) REVERT: B 231 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8843 (m) REVERT: B 240 MET cc_start: 0.9156 (tmm) cc_final: 0.8300 (tmm) REVERT: B 296 ILE cc_start: 0.9274 (mp) cc_final: 0.8847 (tt) REVERT: C 39 LYS cc_start: 0.9239 (mmmm) cc_final: 0.8723 (tmtt) REVERT: C 47 LYS cc_start: 0.8744 (tppt) cc_final: 0.8372 (tppt) REVERT: C 65 ASP cc_start: 0.8405 (t0) cc_final: 0.8001 (t0) REVERT: C 84 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9068 (tt) REVERT: C 160 ASN cc_start: 0.9186 (m-40) cc_final: 0.8812 (m110) REVERT: C 169 MET cc_start: 0.8995 (ttm) cc_final: 0.8659 (ttm) REVERT: C 170 LYS cc_start: 0.9508 (tptm) cc_final: 0.9207 (tttm) REVERT: C 179 GLU cc_start: 0.8563 (mp0) cc_final: 0.8261 (mp0) REVERT: C 214 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8262 (t) REVERT: C 240 MET cc_start: 0.7849 (tmm) cc_final: 0.7148 (tmm) REVERT: C 247 ASN cc_start: 0.8708 (p0) cc_final: 0.8203 (p0) REVERT: C 262 ASP cc_start: 0.8920 (t0) cc_final: 0.8675 (t70) REVERT: D 55 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8700 (t80) REVERT: D 56 LEU cc_start: 0.9364 (tp) cc_final: 0.9026 (tt) REVERT: D 65 ASP cc_start: 0.8944 (t0) cc_final: 0.8734 (t70) REVERT: D 88 MET cc_start: 0.8605 (tmm) cc_final: 0.7853 (tmm) REVERT: D 163 MET cc_start: 0.9265 (mmm) cc_final: 0.8901 (mmm) REVERT: D 170 LYS cc_start: 0.9256 (tptp) cc_final: 0.8672 (tptt) REVERT: D 179 GLU cc_start: 0.8138 (tp30) cc_final: 0.7792 (tp30) REVERT: D 262 ASP cc_start: 0.8992 (t0) cc_final: 0.8791 (t70) REVERT: D 288 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7643 (tt0) REVERT: D 292 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8005 (tm-30) REVERT: E 10 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: E 30 ASP cc_start: 0.8852 (m-30) cc_final: 0.8557 (m-30) REVERT: E 73 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8798 (p0) REVERT: E 108 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: E 153 ILE cc_start: 0.9530 (mm) cc_final: 0.9198 (mm) REVERT: E 271 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8097 (m-10) REVERT: E 419 CYS cc_start: 0.9267 (m) cc_final: 0.9029 (t) REVERT: E 486 GLN cc_start: 0.9667 (OUTLIER) cc_final: 0.9431 (mm110) REVERT: E 503 MET cc_start: 0.9257 (tpt) cc_final: 0.8935 (tpt) REVERT: E 584 PHE cc_start: 0.8904 (m-80) cc_final: 0.8456 (m-80) REVERT: E 1080 LEU cc_start: 0.9347 (tp) cc_final: 0.9017 (mt) REVERT: E 1110 MET cc_start: 0.8625 (mtp) cc_final: 0.8261 (mmm) REVERT: E 1129 CYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8141 (p) REVERT: E 1143 LEU cc_start: 0.9617 (tp) cc_final: 0.9282 (pp) REVERT: E 1280 LEU cc_start: 0.9240 (mm) cc_final: 0.8890 (tp) REVERT: E 1395 MET cc_start: 0.9007 (mmm) cc_final: 0.8717 (mmm) outliers start: 105 outliers final: 73 residues processed: 406 average time/residue: 0.1320 time to fit residues: 87.5400 Evaluate side-chains 383 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 300 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 775 GLN Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1064 TYR Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1239 LEU Chi-restraints excluded: chain E residue 1258 CYS Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1375 ILE Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [219, 108, 91, 12, 141, 22, 256, 119, 154, 47, 123] chunk 219 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 256 optimal weight: 0.9990 chunk 119 optimal weight: 0.2980 chunk 154 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN D 259 HIS E 11 ASN E 60 HIS E 73 ASN ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1234 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.055444 restraints weight = 91097.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.057159 restraints weight = 45460.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.058311 restraints weight = 28213.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.059098 restraints weight = 20144.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.059593 restraints weight = 15802.764| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21615 Z= 0.120 Angle : 0.626 11.741 29373 Z= 0.309 Chirality : 0.043 0.187 3474 Planarity : 0.003 0.062 3650 Dihedral : 5.511 100.847 2888 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.04 % Allowed : 23.70 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.16), residues: 2663 helix: 0.79 (0.14), residues: 1396 sheet: -0.14 (0.33), residues: 254 loop : -1.23 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1579 TYR 0.013 0.001 TYR B 304 PHE 0.027 0.001 PHE E 364 TRP 0.017 0.001 TRP B 83 HIS 0.005 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (21611) covalent geometry : angle 0.62495 / 0.31 (29365) SS BOND : bond 0.00253 / 0.13 ( 4) SS BOND : angle 1.98857 / 1.24 ( 8) hydrogen bonds : bond 0.03793 / 2.49 ( 1148) hydrogen bonds : angle 4.16462 / 2.95 ( 3384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 343 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9233 (mt) cc_final: 0.8810 (pp) REVERT: A 83 TRP cc_start: 0.9631 (m-10) cc_final: 0.9062 (m-90) REVERT: A 163 MET cc_start: 0.9566 (mmm) cc_final: 0.9290 (mmm) REVERT: B 148 ILE cc_start: 0.9680 (tt) cc_final: 0.9440 (tp) REVERT: B 160 ASN cc_start: 0.9067 (m-40) cc_final: 0.8782 (m110) REVERT: B 162 ILE cc_start: 0.9566 (mm) cc_final: 0.9344 (tp) REVERT: B 185 LYS cc_start: 0.9329 (ttmm) cc_final: 0.8899 (tptt) REVERT: B 231 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8835 (m) REVERT: B 240 MET cc_start: 0.9211 (tmm) cc_final: 0.8906 (tmm) REVERT: B 296 ILE cc_start: 0.9254 (mp) cc_final: 0.8865 (tt) REVERT: B 349 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9092 (mm) REVERT: C 39 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8655 (tmtt) REVERT: C 47 LYS cc_start: 0.8686 (tppt) cc_final: 0.8249 (tppt) REVERT: C 48 ASN cc_start: 0.8597 (m-40) cc_final: 0.7947 (m-40) REVERT: C 65 ASP cc_start: 0.8358 (t0) cc_final: 0.7978 (t0) REVERT: C 84 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9042 (tt) REVERT: C 160 ASN cc_start: 0.9139 (m-40) cc_final: 0.8768 (m110) REVERT: C 169 MET cc_start: 0.8949 (ttm) cc_final: 0.8630 (ttm) REVERT: C 170 LYS cc_start: 0.9456 (tptm) cc_final: 0.9175 (tttm) REVERT: C 179 GLU cc_start: 0.8522 (mp0) cc_final: 0.8178 (mp0) REVERT: C 214 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8719 (t) REVERT: C 240 MET cc_start: 0.7696 (tmm) cc_final: 0.7090 (tmm) REVERT: C 262 ASP cc_start: 0.8904 (t0) cc_final: 0.8656 (t0) REVERT: C 288 GLU cc_start: 0.8620 (mm-30) cc_final: 0.7927 (mm-30) REVERT: C 338 LYS cc_start: 0.9191 (tppt) cc_final: 0.8941 (tppt) REVERT: D 56 LEU cc_start: 0.9346 (tp) cc_final: 0.8993 (tt) REVERT: D 65 ASP cc_start: 0.8900 (t0) cc_final: 0.8675 (t70) REVERT: D 77 MET cc_start: 0.8356 (tpp) cc_final: 0.7650 (tpp) REVERT: D 88 MET cc_start: 0.8545 (tmm) cc_final: 0.7821 (tmm) REVERT: D 160 ASN cc_start: 0.9084 (m-40) cc_final: 0.8804 (t0) REVERT: D 163 MET cc_start: 0.9271 (mmm) cc_final: 0.8954 (mmm) REVERT: D 164 LEU cc_start: 0.9580 (mt) cc_final: 0.9283 (mt) REVERT: D 170 LYS cc_start: 0.9208 (tptp) cc_final: 0.8574 (tptm) REVERT: D 179 GLU cc_start: 0.8094 (tp30) cc_final: 0.7775 (tp30) REVERT: D 288 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7654 (tt0) REVERT: D 292 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7997 (tm-30) REVERT: E 30 ASP cc_start: 0.8821 (m-30) cc_final: 0.8514 (m-30) REVERT: E 62 HIS cc_start: 0.8389 (t-90) cc_final: 0.8028 (t-90) REVERT: E 73 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8779 (p0) REVERT: E 105 LEU cc_start: 0.9454 (mt) cc_final: 0.9213 (mt) REVERT: E 108 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: E 116 MET cc_start: 0.9277 (mmm) cc_final: 0.9074 (tpp) REVERT: E 153 ILE cc_start: 0.9513 (mm) cc_final: 0.9213 (mm) REVERT: E 271 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8190 (m-10) REVERT: E 419 CYS cc_start: 0.9215 (m) cc_final: 0.8967 (t) REVERT: E 486 GLN cc_start: 0.9651 (OUTLIER) cc_final: 0.9423 (mm110) REVERT: E 503 MET cc_start: 0.9217 (tpt) cc_final: 0.8895 (tpt) REVERT: E 584 PHE cc_start: 0.8871 (m-80) cc_final: 0.8377 (m-80) REVERT: E 611 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9267 (mm) REVERT: E 1143 LEU cc_start: 0.9613 (tp) cc_final: 0.9264 (pp) REVERT: E 1188 ASP cc_start: 0.8565 (t70) cc_final: 0.8218 (t0) REVERT: E 1280 LEU cc_start: 0.9218 (mm) cc_final: 0.8817 (tp) REVERT: E 1455 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9136 (pp) outliers start: 93 outliers final: 67 residues processed: 414 average time/residue: 0.1346 time to fit residues: 90.2842 Evaluate side-chains 390 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 313 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 775 GLN Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1064 TYR Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1239 LEU Chi-restraints excluded: chain E residue 1258 CYS Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1375 ILE Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [208, 155, 18, 13, 215, 222, 52, 4, 90, 7, 248] chunk 208 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 248 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN E 563 HIS ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.055316 restraints weight = 91103.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.057017 restraints weight = 45741.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.058173 restraints weight = 28475.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.058946 restraints weight = 20391.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.059478 restraints weight = 16079.359| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21615 Z= 0.132 Angle : 0.632 11.639 29373 Z= 0.313 Chirality : 0.043 0.193 3474 Planarity : 0.004 0.061 3650 Dihedral : 5.482 101.833 2887 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.08 % Allowed : 24.18 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2663 helix: 0.85 (0.14), residues: 1396 sheet: -0.08 (0.33), residues: 254 loop : -1.16 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 206 TYR 0.011 0.001 TYR E 231 PHE 0.028 0.001 PHE E 364 TRP 0.018 0.001 TRP B 83 HIS 0.005 0.001 HIS E 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (21611) covalent geometry : angle 0.63085 / 0.31 (29365) SS BOND : bond 0.00260 / 0.13 ( 4) SS BOND : angle 1.96724 / 1.23 ( 8) hydrogen bonds : bond 0.03797 / 2.49 ( 1148) hydrogen bonds : angle 4.14720 / 2.93 ( 3384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 329 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9267 (mt) cc_final: 0.8846 (pp) REVERT: A 83 TRP cc_start: 0.9621 (m-10) cc_final: 0.9057 (m-90) REVERT: A 163 MET cc_start: 0.9571 (mmm) cc_final: 0.9308 (mmm) REVERT: B 148 ILE cc_start: 0.9679 (tt) cc_final: 0.9448 (tp) REVERT: B 160 ASN cc_start: 0.9091 (m-40) cc_final: 0.8791 (m110) REVERT: B 185 LYS cc_start: 0.9312 (ttmm) cc_final: 0.8899 (tptt) REVERT: B 231 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8837 (m) REVERT: B 240 MET cc_start: 0.9204 (tmm) cc_final: 0.8514 (tmm) REVERT: B 296 ILE cc_start: 0.9256 (mp) cc_final: 0.8793 (tt) REVERT: B 349 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9091 (mm) REVERT: C 39 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8675 (tmtt) REVERT: C 47 LYS cc_start: 0.8648 (tppt) cc_final: 0.8238 (tppt) REVERT: C 48 ASN cc_start: 0.8597 (m-40) cc_final: 0.7909 (m-40) REVERT: C 65 ASP cc_start: 0.8362 (t0) cc_final: 0.7992 (t0) REVERT: C 84 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9074 (tt) REVERT: C 144 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9113 (tp) REVERT: C 160 ASN cc_start: 0.9088 (m-40) cc_final: 0.8713 (m110) REVERT: C 169 MET cc_start: 0.8948 (ttm) cc_final: 0.8631 (ttm) REVERT: C 179 GLU cc_start: 0.8452 (mp0) cc_final: 0.7793 (mp0) REVERT: C 214 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8781 (t) REVERT: C 240 MET cc_start: 0.7816 (tmm) cc_final: 0.7080 (tmm) REVERT: C 262 ASP cc_start: 0.8979 (t0) cc_final: 0.8705 (t0) REVERT: C 338 LYS cc_start: 0.9213 (tppt) cc_final: 0.8798 (tptp) REVERT: D 56 LEU cc_start: 0.9342 (tp) cc_final: 0.8980 (tt) REVERT: D 65 ASP cc_start: 0.8909 (t0) cc_final: 0.8670 (t70) REVERT: D 77 MET cc_start: 0.8371 (tpp) cc_final: 0.7627 (tpp) REVERT: D 88 MET cc_start: 0.8551 (tmm) cc_final: 0.7826 (tmm) REVERT: D 128 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8679 (tt0) REVERT: D 160 ASN cc_start: 0.9107 (m-40) cc_final: 0.8789 (t0) REVERT: D 163 MET cc_start: 0.9241 (mmm) cc_final: 0.8903 (mmm) REVERT: D 164 LEU cc_start: 0.9596 (mt) cc_final: 0.9302 (mt) REVERT: D 170 LYS cc_start: 0.9219 (tptp) cc_final: 0.8632 (tptt) REVERT: D 288 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7672 (tt0) REVERT: E 30 ASP cc_start: 0.8832 (m-30) cc_final: 0.8527 (m-30) REVERT: E 62 HIS cc_start: 0.8392 (t-90) cc_final: 0.8032 (t-90) REVERT: E 105 LEU cc_start: 0.9443 (mt) cc_final: 0.9195 (mt) REVERT: E 108 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: E 116 MET cc_start: 0.9321 (mmm) cc_final: 0.9086 (tpp) REVERT: E 153 ILE cc_start: 0.9512 (mm) cc_final: 0.9218 (mm) REVERT: E 271 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8174 (m-10) REVERT: E 486 GLN cc_start: 0.9660 (OUTLIER) cc_final: 0.9455 (mm110) REVERT: E 503 MET cc_start: 0.9216 (tpt) cc_final: 0.8889 (tpt) REVERT: E 584 PHE cc_start: 0.8871 (m-80) cc_final: 0.8482 (m-80) REVERT: E 611 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9268 (mm) REVERT: E 1080 LEU cc_start: 0.9319 (tp) cc_final: 0.8949 (mt) REVERT: E 1110 MET cc_start: 0.8547 (mtp) cc_final: 0.8156 (mmm) REVERT: E 1143 LEU cc_start: 0.9616 (tp) cc_final: 0.9284 (pp) REVERT: E 1188 ASP cc_start: 0.8589 (t70) cc_final: 0.8252 (t0) REVERT: E 1191 GLN cc_start: 0.9150 (tp40) cc_final: 0.8945 (tp-100) REVERT: E 1280 LEU cc_start: 0.9225 (mm) cc_final: 0.8839 (tp) outliers start: 94 outliers final: 74 residues processed: 401 average time/residue: 0.1307 time to fit residues: 85.5181 Evaluate side-chains 398 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 314 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 486 GLN Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 775 GLN Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1064 TYR Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1239 LEU Chi-restraints excluded: chain E residue 1258 CYS Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1375 ILE Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1532 THR Chi-restraints excluded: chain E residue 1581 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [108, 77, 1, 152, 131, 258, 253, 208, 179, 157, 168] chunk 108 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 258 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 208 optimal weight: 0.0980 chunk 179 optimal weight: 7.9990 chunk 157 optimal weight: 0.2980 chunk 168 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.056616 restraints weight = 90218.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.058343 restraints weight = 45566.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.059507 restraints weight = 28526.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.060307 restraints weight = 20400.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.060818 restraints weight = 16054.992| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21615 Z= 0.115 Angle : 0.642 11.834 29373 Z= 0.315 Chirality : 0.043 0.221 3474 Planarity : 0.003 0.062 3650 Dihedral : 5.406 101.826 2886 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.39 % Allowed : 25.39 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2663 helix: 0.92 (0.14), residues: 1395 sheet: -0.22 (0.32), residues: 278 loop : -1.09 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 206 TYR 0.012 0.001 TYR D 330 PHE 0.027 0.001 PHE E 364 TRP 0.015 0.001 TRP B 83 HIS 0.004 0.001 HIS D 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (21611) covalent geometry : angle 0.64158 / 0.31 (29365) SS BOND : bond 0.00208 / 0.11 ( 4) SS BOND : angle 1.74636 / 1.10 ( 8) hydrogen bonds : bond 0.03717 / 2.45 ( 1148) hydrogen bonds : angle 4.10872 / 2.90 ( 3384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 352 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9227 (mt) cc_final: 0.8788 (pp) REVERT: A 83 TRP cc_start: 0.9576 (m-10) cc_final: 0.9057 (m-90) REVERT: A 163 MET cc_start: 0.9548 (mmm) cc_final: 0.9278 (mmm) REVERT: A 292 GLU cc_start: 0.8605 (tp30) cc_final: 0.8242 (tm-30) REVERT: A 293 THR cc_start: 0.9367 (p) cc_final: 0.9098 (p) REVERT: B 160 ASN cc_start: 0.9080 (m-40) cc_final: 0.8774 (m110) REVERT: B 162 ILE cc_start: 0.9529 (mm) cc_final: 0.9295 (tp) REVERT: B 185 LYS cc_start: 0.9306 (ttmm) cc_final: 0.8958 (tptt) REVERT: B 231 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8834 (m) REVERT: B 240 MET cc_start: 0.9182 (tmm) cc_final: 0.8879 (tmm) REVERT: B 250 PHE cc_start: 0.8343 (t80) cc_final: 0.8136 (t80) REVERT: B 296 ILE cc_start: 0.9229 (mp) cc_final: 0.8768 (tt) REVERT: B 349 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9113 (mm) REVERT: C 39 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8707 (tttm) REVERT: C 65 ASP cc_start: 0.8310 (t0) cc_final: 0.7921 (t0) REVERT: C 84 LEU cc_start: 0.9295 (mt) cc_final: 0.9012 (tt) REVERT: C 126 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8329 (mt-10) REVERT: C 144 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9068 (tp) REVERT: C 160 ASN cc_start: 0.9106 (m-40) cc_final: 0.8744 (m110) REVERT: C 169 MET cc_start: 0.8883 (ttm) cc_final: 0.8555 (ttm) REVERT: C 179 GLU cc_start: 0.8450 (mp0) cc_final: 0.7987 (mp0) REVERT: C 199 MET cc_start: 0.8753 (mtm) cc_final: 0.7952 (mpp) REVERT: C 214 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8013 (t) REVERT: C 240 MET cc_start: 0.7539 (tmm) cc_final: 0.7004 (tmm) REVERT: C 247 ASN cc_start: 0.8313 (p0) cc_final: 0.7682 (p0) REVERT: C 262 ASP cc_start: 0.8958 (t0) cc_final: 0.8664 (t0) REVERT: C 338 LYS cc_start: 0.9222 (tppt) cc_final: 0.9000 (tppt) REVERT: D 56 LEU cc_start: 0.9319 (tp) cc_final: 0.9003 (tt) REVERT: D 65 ASP cc_start: 0.8899 (t0) cc_final: 0.8645 (t70) REVERT: D 88 MET cc_start: 0.8517 (tmm) cc_final: 0.7794 (tmm) REVERT: D 128 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8558 (tt0) REVERT: D 160 ASN cc_start: 0.9023 (m-40) cc_final: 0.8773 (t0) REVERT: D 163 MET cc_start: 0.9257 (mmm) cc_final: 0.8954 (mmm) REVERT: D 164 LEU cc_start: 0.9568 (mt) cc_final: 0.9284 (mt) REVERT: D 170 LYS cc_start: 0.9163 (tptp) cc_final: 0.8624 (tptt) REVERT: D 288 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7696 (tt0) REVERT: E 30 ASP cc_start: 0.8842 (m-30) cc_final: 0.8509 (m-30) REVERT: E 62 HIS cc_start: 0.8325 (t-90) cc_final: 0.7990 (t-90) REVERT: E 105 LEU cc_start: 0.9406 (mt) cc_final: 0.9137 (mt) REVERT: E 108 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7856 (m-10) REVERT: E 153 ILE cc_start: 0.9475 (mm) cc_final: 0.9184 (mm) REVERT: E 271 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8139 (m-10) REVERT: E 358 VAL cc_start: 0.9194 (m) cc_final: 0.8846 (p) REVERT: E 503 MET cc_start: 0.9139 (tpt) cc_final: 0.8828 (tpt) REVERT: E 584 PHE cc_start: 0.8860 (m-80) cc_final: 0.8603 (m-80) REVERT: E 611 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9267 (mm) REVERT: E 790 PHE cc_start: 0.8496 (t80) cc_final: 0.8261 (t80) REVERT: E 1107 LEU cc_start: 0.9369 (mt) cc_final: 0.9015 (tt) REVERT: E 1143 LEU cc_start: 0.9614 (tp) cc_final: 0.9281 (pp) REVERT: E 1188 ASP cc_start: 0.8411 (t70) cc_final: 0.7946 (t0) REVERT: E 1280 LEU cc_start: 0.9045 (mm) cc_final: 0.8709 (tp) REVERT: E 1455 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9117 (pp) outliers start: 78 outliers final: 60 residues processed: 410 average time/residue: 0.1300 time to fit residues: 86.8527 Evaluate side-chains 388 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 319 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 775 GLN Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1064 TYR Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1239 LEU Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1375 ILE Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [100, 176, 67, 109, 24, 127, 65, 223, 205, 261, 183] chunk 100 optimal weight: 0.9980 chunk 176 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 65 optimal weight: 0.0970 chunk 223 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 153 ASN C 335 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN E 327 HIS ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1439 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.056462 restraints weight = 90503.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.058167 restraints weight = 45948.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.059332 restraints weight = 28813.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.060148 restraints weight = 20663.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.060668 restraints weight = 16173.869| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21615 Z= 0.119 Angle : 0.652 12.656 29373 Z= 0.318 Chirality : 0.043 0.256 3474 Planarity : 0.004 0.062 3650 Dihedral : 5.368 101.125 2886 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.95 % Allowed : 26.22 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.16), residues: 2663 helix: 0.94 (0.14), residues: 1396 sheet: -0.15 (0.32), residues: 278 loop : -1.04 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 206 TYR 0.012 0.001 TYR E1254 PHE 0.024 0.001 PHE E 133 TRP 0.015 0.001 TRP B 83 HIS 0.004 0.000 HIS E 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (21611) covalent geometry : angle 0.65152 / 0.32 (29365) SS BOND : bond 0.00198 / 0.10 ( 4) SS BOND : angle 1.67120 / 1.05 ( 8) hydrogen bonds : bond 0.03671 / 2.41 ( 1148) hydrogen bonds : angle 4.08633 / 2.89 ( 3384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 341 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9227 (mt) cc_final: 0.8788 (pp) REVERT: A 77 MET cc_start: 0.8691 (mmm) cc_final: 0.8352 (mmm) REVERT: A 83 TRP cc_start: 0.9553 (m-10) cc_final: 0.9064 (m-90) REVERT: A 163 MET cc_start: 0.9531 (mmm) cc_final: 0.9267 (mmm) REVERT: A 292 GLU cc_start: 0.8621 (tp30) cc_final: 0.8356 (tm-30) REVERT: A 293 THR cc_start: 0.9379 (p) cc_final: 0.9099 (p) REVERT: B 77 MET cc_start: 0.8914 (tpp) cc_final: 0.8409 (ttt) REVERT: B 160 ASN cc_start: 0.9101 (m-40) cc_final: 0.8789 (m110) REVERT: B 185 LYS cc_start: 0.9317 (ttmm) cc_final: 0.8909 (tptt) REVERT: B 199 MET cc_start: 0.8265 (mtt) cc_final: 0.7219 (mtt) REVERT: B 231 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8815 (m) REVERT: B 240 MET cc_start: 0.9176 (tmm) cc_final: 0.8854 (tmm) REVERT: B 250 PHE cc_start: 0.8309 (t80) cc_final: 0.8085 (t80) REVERT: B 296 ILE cc_start: 0.9221 (mp) cc_final: 0.8763 (tt) REVERT: B 349 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9074 (mm) REVERT: C 39 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8695 (tttm) REVERT: C 65 ASP cc_start: 0.8378 (t0) cc_final: 0.8005 (t0) REVERT: C 84 LEU cc_start: 0.9258 (mt) cc_final: 0.8983 (tt) REVERT: C 126 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8194 (mt-10) REVERT: C 144 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9123 (tp) REVERT: C 160 ASN cc_start: 0.9055 (m-40) cc_final: 0.8663 (m110) REVERT: C 169 MET cc_start: 0.8866 (ttm) cc_final: 0.8521 (ttm) REVERT: C 179 GLU cc_start: 0.8408 (mp0) cc_final: 0.7752 (mp0) REVERT: C 199 MET cc_start: 0.8782 (mtm) cc_final: 0.7927 (mpp) REVERT: C 214 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.7960 (t) REVERT: C 240 MET cc_start: 0.7519 (tmm) cc_final: 0.6933 (tmm) REVERT: C 247 ASN cc_start: 0.8285 (p0) cc_final: 0.7707 (p0) REVERT: C 262 ASP cc_start: 0.8968 (t0) cc_final: 0.8661 (t70) REVERT: C 338 LYS cc_start: 0.9231 (tppt) cc_final: 0.8663 (tptp) REVERT: D 56 LEU cc_start: 0.9340 (tp) cc_final: 0.9010 (tt) REVERT: D 65 ASP cc_start: 0.8917 (t0) cc_final: 0.8649 (t70) REVERT: D 77 MET cc_start: 0.8346 (tpp) cc_final: 0.7566 (tpp) REVERT: D 88 MET cc_start: 0.8518 (tmm) cc_final: 0.7790 (tmm) REVERT: D 128 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8993 (tt0) REVERT: D 160 ASN cc_start: 0.8994 (m-40) cc_final: 0.8787 (t0) REVERT: D 163 MET cc_start: 0.9275 (mmm) cc_final: 0.8993 (mmm) REVERT: D 164 LEU cc_start: 0.9586 (mt) cc_final: 0.9299 (mt) REVERT: D 170 LYS cc_start: 0.9162 (tptp) cc_final: 0.8545 (tptm) REVERT: D 209 MET cc_start: 0.8859 (mmm) cc_final: 0.8449 (mmm) REVERT: D 288 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7793 (tt0) REVERT: E 30 ASP cc_start: 0.8851 (m-30) cc_final: 0.8521 (m-30) REVERT: E 62 HIS cc_start: 0.8293 (t-90) cc_final: 0.7983 (t-90) REVERT: E 80 PHE cc_start: 0.8388 (m-80) cc_final: 0.8103 (m-80) REVERT: E 105 LEU cc_start: 0.9343 (mt) cc_final: 0.9056 (mt) REVERT: E 108 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7861 (m-10) REVERT: E 116 MET cc_start: 0.9247 (mmm) cc_final: 0.9033 (tpp) REVERT: E 153 ILE cc_start: 0.9458 (mm) cc_final: 0.9168 (mm) REVERT: E 271 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8109 (m-10) REVERT: E 358 VAL cc_start: 0.9190 (m) cc_final: 0.8836 (p) REVERT: E 503 MET cc_start: 0.9177 (tpt) cc_final: 0.8847 (tpt) REVERT: E 584 PHE cc_start: 0.8856 (m-80) cc_final: 0.8602 (m-80) REVERT: E 611 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9250 (mm) REVERT: E 790 PHE cc_start: 0.8592 (t80) cc_final: 0.8384 (t80) REVERT: E 1080 LEU cc_start: 0.9303 (tp) cc_final: 0.8931 (mt) REVERT: E 1123 ASN cc_start: 0.9473 (t0) cc_final: 0.9127 (t0) REVERT: E 1143 LEU cc_start: 0.9601 (tp) cc_final: 0.9299 (pp) REVERT: E 1188 ASP cc_start: 0.8361 (t70) cc_final: 0.7947 (t0) REVERT: E 1280 LEU cc_start: 0.8965 (mm) cc_final: 0.8671 (tp) outliers start: 68 outliers final: 54 residues processed: 391 average time/residue: 0.1301 time to fit residues: 83.5937 Evaluate side-chains 390 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 328 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 775 GLN Chi-restraints excluded: chain E residue 1027 LEU Chi-restraints excluded: chain E residue 1064 TYR Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1239 LEU Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1375 ILE Chi-restraints excluded: chain E residue 1497 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [186, 245, 61, 250, 196, 21, 247, 16, 189, 212, 133] chunk 186 optimal weight: 0.6980 chunk 245 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 250 optimal weight: 8.9990 chunk 196 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 247 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 278 HIS ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 HIS C 153 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN E 106 HIS E 327 HIS ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.064038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.053090 restraints weight = 91677.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.054725 restraints weight = 46969.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.055864 restraints weight = 29558.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.056630 restraints weight = 21166.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.057043 restraints weight = 16714.781| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 21615 Z= 0.202 Angle : 0.695 11.977 29373 Z= 0.346 Chirality : 0.045 0.222 3474 Planarity : 0.004 0.059 3650 Dihedral : 5.534 107.765 2886 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.04 % Allowed : 26.61 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.16), residues: 2663 helix: 0.95 (0.14), residues: 1381 sheet: -0.02 (0.32), residues: 268 loop : -0.84 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 206 TYR 0.014 0.001 TYR C 268 PHE 0.028 0.002 PHE E 133 TRP 0.020 0.002 TRP B 90 HIS 0.005 0.001 HIS E 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (21611) covalent geometry : angle 0.69444 / 0.35 (29365) SS BOND : bond 0.00314 / 0.16 ( 4) SS BOND : angle 1.93689 / 1.22 ( 8) hydrogen bonds : bond 0.03978 / 2.63 ( 1148) hydrogen bonds : angle 4.23320 / 2.99 ( 3384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.27 seconds wall clock time: 59 minutes 4.37 seconds (3544.37 seconds total)