Starting phenix.real_space_refine on Thu Mar 5 10:35:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s5z_24844/03_2026/7s5z_24844.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5z_24844/03_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_24844/03_2026/7s5z_24844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5z_24844/03_2026/7s5z_24844.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s5z_24844/03_2026/7s5z_24844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5z_24844/03_2026/7s5z_24844.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 4.58, per 1000 atoms: 0.22 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=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" C CYS D 344 " - pdb=" SG CYS D 344 " distance=2.89 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: 1.67 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.82 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: 5.02 Time building geometry restraints manager: 2.26 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: 11958 26.38 - 52.75: 765 52.75 - 79.13: 117 79.13 - 105.50: 7 105.50 - 131.88: 1 Dihedral angle restraints: 12848 sinusoidal: 5045 harmonic: 7803 Sorted by residual: dihedral pdb=" CB CYS D 344 " pdb=" C CYS D 344 " pdb=" SG CYS D 344 " pdb=" CB CYS D 344 " ideal model delta sinusoidal sigma weight residual -86.00 -0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 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 ... (remaining 12845 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: 19062 3.20 - 3.77: 35649 3.77 - 4.33: 45499 4.33 - 4.90: 73763 Nonbonded interactions: 174310 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 174305 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: 3.550 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.740 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:1.460 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: 0.8359 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 : 0.008 0.855 21616 Z= 0.403 Angle : 1.067 66.611 29375 Z= 0.588 Chirality : 0.056 0.311 3474 Planarity : 0.007 0.069 3650 Dihedral : 16.842 131.879 7763 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 covalent geometry : bond 0.00535 (21611) covalent geometry : angle 0.96026 (29365) SS BOND : bond 0.38256 ( 5) SS BOND : angle 25.27643 ( 10) hydrogen bonds : bond 0.15788 ( 1148) hydrogen bonds : angle 6.74386 ( 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 : 0.826 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: 0.1543 time to fit residues: 149.3091 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 : 0.877 ------------------------------------------------------------------------------- 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: 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3192 r_free = 0.3192 target = 0.064611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.053739 restraints weight = 91720.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.055430 restraints weight = 45462.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056570 restraints weight = 28214.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057345 restraints weight = 20176.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.057862 restraints weight = 15860.827| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 21616 Z= 0.169 Angle : 0.755 52.592 29375 Z= 0.386 Chirality : 0.044 0.240 3474 Planarity : 0.005 0.060 3650 Dihedral : 7.862 111.764 2979 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.30 % Allowed : 17.23 % Favored : 79.47 % 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: -1.56 (0.15), residues: 2663 helix: -0.33 (0.13), residues: 1362 sheet: -1.41 (0.31), residues: 242 loop : -1.77 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 835 TYR 0.014 0.001 TYR E 379 PHE 0.027 0.002 PHE E1503 TRP 0.015 0.001 TRP A 311 HIS 0.005 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00371 (21611) covalent geometry : angle 0.66722 (29365) SS BOND : bond 0.01776 ( 5) SS BOND : angle 19.13686 ( 10) hydrogen bonds : bond 0.04422 ( 1148) hydrogen bonds : angle 4.72193 ( 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 448 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 372 time to evaluate : 0.909 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: 0.9311 (m) cc_final: 0.9011 (t) REVERT: A 66 LEU cc_start: 0.9071 (mt) cc_final: 0.8764 (mt) REVERT: A 83 TRP cc_start: 0.9578 (m-10) cc_final: 0.8957 (m-90) REVERT: A 141 GLU cc_start: 0.8737 (tp30) cc_final: 0.8338 (tp30) REVERT: A 163 MET cc_start: 0.9564 (mmm) cc_final: 0.9235 (mmm) REVERT: A 170 LYS cc_start: 0.9499 (tptp) cc_final: 0.9083 (tptt) REVERT: A 268 TYR cc_start: 0.9010 (t80) cc_final: 0.8716 (t80) REVERT: A 330 TYR cc_start: 0.8754 (m-80) cc_final: 0.8541 (m-80) REVERT: B 80 LEU cc_start: 0.9663 (mm) cc_final: 0.9447 (mp) REVERT: B 160 ASN cc_start: 0.9195 (m-40) cc_final: 0.8933 (m-40) REVERT: B 179 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8503 (mt-10) REVERT: B 185 LYS cc_start: 0.9199 (ttmm) cc_final: 0.8599 (tptp) REVERT: B 240 MET cc_start: 0.9288 (tmm) cc_final: 0.8701 (tmm) REVERT: B 296 ILE cc_start: 0.9182 (mp) cc_final: 0.8952 (tt) REVERT: C 39 LYS cc_start: 0.9305 (mmmm) cc_final: 0.8760 (tmtt) REVERT: C 47 LYS cc_start: 0.8276 (tppt) cc_final: 0.7918 (tppt) REVERT: C 63 LEU cc_start: 0.9638 (tp) cc_final: 0.9325 (tt) REVERT: C 65 ASP cc_start: 0.8396 (t0) cc_final: 0.8051 (t0) REVERT: C 84 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9008 (tt) REVERT: C 160 ASN cc_start: 0.9204 (m-40) cc_final: 0.8765 (m110) REVERT: C 169 MET cc_start: 0.8974 (ttm) cc_final: 0.8718 (ttm) REVERT: C 170 LYS cc_start: 0.9443 (tptm) cc_final: 0.9202 (tttp) REVERT: C 179 GLU cc_start: 0.8506 (mp0) cc_final: 0.8046 (mp0) REVERT: C 185 LYS cc_start: 0.9360 (mmtm) cc_final: 0.9027 (mmtm) REVERT: C 214 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.8672 (t) REVERT: C 240 MET cc_start: 0.8563 (tmm) cc_final: 0.8210 (tmm) REVERT: C 247 ASN cc_start: 0.8779 (p0) cc_final: 0.8512 (p0) REVERT: C 279 GLN cc_start: 0.8985 (tp40) cc_final: 0.8163 (tm-30) REVERT: D 65 ASP cc_start: 0.8973 (t0) cc_final: 0.8663 (t70) REVERT: D 77 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8303 (tpp) REVERT: D 163 MET cc_start: 0.9186 (mmm) cc_final: 0.8809 (mmm) REVERT: D 170 LYS cc_start: 0.9146 (tptp) cc_final: 0.8911 (tptt) REVERT: D 179 GLU cc_start: 0.8131 (tp30) cc_final: 0.7876 (tp30) REVERT: D 262 ASP cc_start: 0.9152 (t0) cc_final: 0.8898 (t70) REVERT: D 293 THR cc_start: 0.9308 (p) cc_final: 0.8923 (p) REVERT: D 335 ASN cc_start: 0.8602 (t0) cc_final: 0.8385 (t0) REVERT: E 30 ASP cc_start: 0.8789 (m-30) cc_final: 0.8459 (m-30) REVERT: E 80 PHE cc_start: 0.8705 (m-80) cc_final: 0.8368 (m-80) REVERT: E 153 ILE cc_start: 0.9507 (mm) cc_final: 0.9242 (mm) REVERT: E 442 MET cc_start: 0.8741 (tpt) cc_final: 0.8474 (tpt) REVERT: E 508 LYS cc_start: 0.9523 (tttt) cc_final: 0.9300 (ttmm) REVERT: E 547 MET cc_start: 0.8767 (tmm) cc_final: 0.8456 (tmm) REVERT: E 584 PHE cc_start: 0.8952 (m-80) cc_final: 0.8694 (m-80) REVERT: E 790 PHE cc_start: 0.8645 (t80) cc_final: 0.8410 (t80) REVERT: E 1081 VAL cc_start: 0.9075 (m) cc_final: 0.8870 (p) REVERT: E 1188 ASP cc_start: 0.8583 (t70) cc_final: 0.8156 (t0) REVERT: E 1191 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8718 (tp-100) REVERT: E 1290 MET cc_start: 0.8960 (tpp) cc_final: 0.8628 (mmp) REVERT: E 1305 MET cc_start: 0.9400 (tpt) cc_final: 0.9184 (tpp) REVERT: E 1395 MET cc_start: 0.8742 (mmm) cc_final: 0.8528 (mmm) REVERT: E 1402 HIS cc_start: 0.8230 (m-70) cc_final: 0.7435 (t-170) REVERT: E 1404 ILE cc_start: 0.9063 (mt) cc_final: 0.8617 (pt) outliers start: 76 outliers final: 43 residues processed: 430 average time/residue: 0.1323 time to fit residues: 91.7696 Evaluate side-chains 358 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 311 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 244 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 84 LEU 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 D residue 344 CYS 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 Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 264 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 C 153 ASN C 173 GLN C 279 GLN D 48 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN E 475 GLN ** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.062637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.051758 restraints weight = 93892.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.053379 restraints weight = 47140.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.054476 restraints weight = 29542.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.055226 restraints weight = 21253.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.055698 restraints weight = 16830.906| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 21616 Z= 0.210 Angle : 0.755 52.264 29375 Z= 0.383 Chirality : 0.044 0.190 3474 Planarity : 0.004 0.063 3650 Dihedral : 6.983 89.507 2930 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.08 % Allowed : 19.18 % Favored : 76.74 % 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: -0.84 (0.16), residues: 2663 helix: 0.35 (0.14), residues: 1365 sheet: -1.05 (0.31), residues: 240 loop : -1.58 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1579 TYR 0.015 0.002 TYR C 268 PHE 0.028 0.002 PHE E1496 TRP 0.022 0.002 TRP A 311 HIS 0.006 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00461 (21611) covalent geometry : angle 0.66799 (29365) SS BOND : bond 0.01863 ( 5) SS BOND : angle 19.06893 ( 10) hydrogen bonds : bond 0.04293 ( 1148) hydrogen bonds : angle 4.51734 ( 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 416 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 322 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TRP cc_start: 0.9617 (m-10) cc_final: 0.9012 (m-90) REVERT: A 163 MET cc_start: 0.9591 (mmm) cc_final: 0.9323 (mmm) REVERT: A 170 LYS cc_start: 0.9510 (tptp) cc_final: 0.9285 (tptm) REVERT: A 332 LYS cc_start: 0.9410 (pttt) cc_final: 0.9096 (ptpp) REVERT: B 160 ASN cc_start: 0.9123 (m-40) cc_final: 0.8833 (m110) REVERT: B 169 MET cc_start: 0.9103 (ttm) cc_final: 0.8778 (ttm) REVERT: B 179 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8476 (mt-10) REVERT: B 185 LYS cc_start: 0.9301 (ttmm) cc_final: 0.8754 (tptp) REVERT: B 240 MET cc_start: 0.9221 (tmm) cc_final: 0.8306 (tmm) REVERT: C 39 LYS cc_start: 0.9331 (mmmm) cc_final: 0.8800 (tmtt) REVERT: C 47 LYS cc_start: 0.8356 (tppt) cc_final: 0.8076 (tppt) REVERT: C 63 LEU cc_start: 0.9637 (tp) cc_final: 0.9423 (tt) REVERT: C 65 ASP cc_start: 0.8559 (t0) cc_final: 0.8127 (t0) REVERT: C 84 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9024 (tt) REVERT: C 160 ASN cc_start: 0.9223 (m-40) cc_final: 0.8801 (m110) REVERT: C 163 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.9052 (mmt) REVERT: C 169 MET cc_start: 0.9053 (ttm) cc_final: 0.8740 (ttm) REVERT: C 170 LYS cc_start: 0.9493 (tptm) cc_final: 0.9128 (tttm) REVERT: C 179 GLU cc_start: 0.8584 (mp0) cc_final: 0.8041 (mp0) REVERT: C 214 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.8441 (t) REVERT: C 247 ASN cc_start: 0.8785 (p0) cc_final: 0.8338 (p0) REVERT: C 332 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9073 (pttp) REVERT: D 55 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8694 (t80) REVERT: D 65 ASP cc_start: 0.9000 (t0) cc_final: 0.8661 (t70) REVERT: D 77 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8580 (tpp) REVERT: D 88 MET cc_start: 0.8538 (tmm) cc_final: 0.7958 (tmm) REVERT: D 163 MET cc_start: 0.9197 (mmm) cc_final: 0.8763 (mmm) REVERT: D 170 LYS cc_start: 0.9305 (tptp) cc_final: 0.8764 (tptt) REVERT: D 179 GLU cc_start: 0.8279 (tp30) cc_final: 0.7779 (tp30) REVERT: D 262 ASP cc_start: 0.9092 (t0) cc_final: 0.8773 (t70) REVERT: D 335 ASN cc_start: 0.8540 (t0) cc_final: 0.8326 (t0) REVERT: E 30 ASP cc_start: 0.8844 (m-30) cc_final: 0.8535 (m-30) REVERT: E 83 LEU cc_start: 0.9581 (mt) cc_final: 0.9340 (mt) REVERT: E 108 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: E 153 ILE cc_start: 0.9532 (mm) cc_final: 0.9245 (mm) REVERT: E 226 LEU cc_start: 0.8739 (tt) cc_final: 0.8511 (tp) REVERT: E 311 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8593 (p0) REVERT: E 442 MET cc_start: 0.8774 (tpt) cc_final: 0.8562 (tpt) REVERT: E 508 LYS cc_start: 0.9517 (tttt) cc_final: 0.9305 (ttmm) REVERT: E 547 MET cc_start: 0.8762 (tmm) cc_final: 0.8190 (tmm) REVERT: E 584 PHE cc_start: 0.9002 (m-80) cc_final: 0.8764 (m-80) REVERT: E 790 PHE cc_start: 0.8665 (t80) cc_final: 0.8372 (t80) REVERT: E 1080 LEU cc_start: 0.9336 (tp) cc_final: 0.9102 (mt) REVERT: E 1191 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8760 (tp-100) REVERT: E 1402 HIS cc_start: 0.8183 (m-70) cc_final: 0.7711 (t-170) outliers start: 94 outliers final: 59 residues processed: 391 average time/residue: 0.1330 time to fit residues: 83.7320 Evaluate side-chains 355 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 288 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 59 VAL 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 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 244 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 328 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 139 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 163 MET 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 77 MET 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 224 THR 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 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 D residue 349 LEU 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 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 702 ILE 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 1228 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 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: chunk 238 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 266 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN E 73 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.064446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.053663 restraints weight = 92210.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.055324 restraints weight = 45672.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.056422 restraints weight = 28325.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.057208 restraints weight = 20214.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.057691 restraints weight = 15806.571| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 21616 Z= 0.181 Angle : 0.734 52.166 29375 Z= 0.367 Chirality : 0.043 0.172 3474 Planarity : 0.004 0.062 3650 Dihedral : 6.711 93.483 2925 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.30 % Allowed : 20.79 % Favored : 74.91 % 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: -0.44 (0.16), residues: 2663 helix: 0.64 (0.14), residues: 1368 sheet: -0.56 (0.31), residues: 246 loop : -1.42 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1579 TYR 0.011 0.001 TYR E 379 PHE 0.025 0.001 PHE E1496 TRP 0.015 0.001 TRP B 83 HIS 0.005 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00398 (21611) covalent geometry : angle 0.64446 (29365) SS BOND : bond 0.01845 ( 5) SS BOND : angle 19.03558 ( 10) hydrogen bonds : bond 0.04144 ( 1148) hydrogen bonds : angle 4.39614 ( 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 427 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 328 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.9584 (mmm) cc_final: 0.9326 (mmm) REVERT: A 170 LYS cc_start: 0.9497 (tptp) cc_final: 0.9273 (tptm) REVERT: B 160 ASN cc_start: 0.9096 (m-40) cc_final: 0.8835 (m-40) REVERT: B 169 MET cc_start: 0.9079 (ttm) cc_final: 0.8614 (ttm) REVERT: B 185 LYS cc_start: 0.9308 (ttmm) cc_final: 0.8828 (tptt) REVERT: B 240 MET cc_start: 0.9236 (tmm) cc_final: 0.8430 (tmm) REVERT: B 242 ASN cc_start: 0.8610 (p0) cc_final: 0.8355 (p0) REVERT: B 296 ILE cc_start: 0.9335 (mp) cc_final: 0.8945 (tt) REVERT: C 39 LYS cc_start: 0.9320 (mmmm) cc_final: 0.8788 (tmtt) REVERT: C 47 LYS cc_start: 0.8286 (tppt) cc_final: 0.8060 (tppt) REVERT: C 65 ASP cc_start: 0.8509 (t0) cc_final: 0.8042 (t0) REVERT: C 84 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9113 (tt) REVERT: C 160 ASN cc_start: 0.9207 (m-40) cc_final: 0.8821 (m110) REVERT: C 169 MET cc_start: 0.9033 (ttm) cc_final: 0.8718 (ttm) REVERT: C 170 LYS cc_start: 0.9489 (tptm) cc_final: 0.9178 (tttm) REVERT: C 179 GLU cc_start: 0.8556 (mp0) cc_final: 0.7991 (mp0) REVERT: C 214 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.8442 (t) REVERT: C 240 MET cc_start: 0.7927 (tmm) cc_final: 0.7065 (tmm) REVERT: C 247 ASN cc_start: 0.8721 (p0) cc_final: 0.8394 (p0) REVERT: C 332 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8958 (pttp) REVERT: C 338 LYS cc_start: 0.9034 (tppt) cc_final: 0.8813 (tptp) REVERT: D 50 ARG cc_start: 0.7497 (mmp-170) cc_final: 0.6670 (mmp80) REVERT: D 55 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8685 (t80) REVERT: D 56 LEU cc_start: 0.9334 (tp) cc_final: 0.9015 (tt) REVERT: D 65 ASP cc_start: 0.8951 (t0) cc_final: 0.8709 (t70) REVERT: D 77 MET cc_start: 0.8764 (ttp) cc_final: 0.8551 (tpp) REVERT: D 88 MET cc_start: 0.8572 (tmm) cc_final: 0.7905 (tmm) REVERT: D 163 MET cc_start: 0.9164 (mmm) cc_final: 0.8758 (mmm) REVERT: D 170 LYS cc_start: 0.9299 (tptp) cc_final: 0.8690 (tptt) REVERT: D 179 GLU cc_start: 0.8119 (tp30) cc_final: 0.7783 (tp30) REVERT: D 262 ASP cc_start: 0.9011 (t0) cc_final: 0.8732 (t70) REVERT: E 30 ASP cc_start: 0.8813 (m-30) cc_final: 0.8529 (m-30) REVERT: E 73 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8760 (p0) REVERT: E 83 LEU cc_start: 0.9582 (mt) cc_final: 0.9356 (mt) REVERT: E 108 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: E 143 TYR cc_start: 0.9511 (t80) cc_final: 0.9249 (t80) REVERT: E 153 ILE cc_start: 0.9549 (mm) cc_final: 0.9255 (mm) REVERT: E 226 LEU cc_start: 0.8869 (tt) cc_final: 0.8661 (tp) REVERT: E 261 LEU cc_start: 0.8985 (tp) cc_final: 0.8673 (tp) REVERT: E 315 PHE cc_start: 0.8384 (m-80) cc_final: 0.8177 (m-80) REVERT: E 442 MET cc_start: 0.8749 (tpt) cc_final: 0.8487 (tpt) REVERT: E 508 LYS cc_start: 0.9498 (tttt) cc_final: 0.9248 (ttmm) REVERT: E 584 PHE cc_start: 0.8960 (m-80) cc_final: 0.8609 (m-80) REVERT: E 591 LEU cc_start: 0.9150 (tp) cc_final: 0.8836 (tp) REVERT: E 611 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9402 (mm) REVERT: E 711 MET cc_start: 0.8045 (mpp) cc_final: 0.7674 (mpp) REVERT: E 790 PHE cc_start: 0.8594 (t80) cc_final: 0.8364 (t80) REVERT: E 877 LEU cc_start: 0.8432 (tp) cc_final: 0.8227 (tt) REVERT: E 1129 CYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8097 (p) REVERT: E 1143 LEU cc_start: 0.9606 (tp) cc_final: 0.9247 (pp) REVERT: E 1191 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8764 (tp-100) REVERT: E 1280 LEU cc_start: 0.9324 (mm) cc_final: 0.9105 (mm) REVERT: E 1402 HIS cc_start: 0.8142 (m-70) cc_final: 0.7889 (t-170) REVERT: E 1524 VAL cc_start: 0.9473 (OUTLIER) cc_final: 0.8887 (p) REVERT: E 1525 MET cc_start: 0.8539 (ptp) cc_final: 0.8169 (ppp) outliers start: 99 outliers final: 56 residues processed: 408 average time/residue: 0.1373 time to fit residues: 90.7332 Evaluate side-chains 362 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 297 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 341 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 115 HIS 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 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 344 CYS Chi-restraints excluded: chain D residue 349 LEU 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 702 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL 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 1198 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 1362 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 1524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 65 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 278 HIS ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 HIS C 46 HIS C 153 ASN D 46 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN D 259 HIS E 106 HIS E 161 HIS ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 896 HIS E1197 GLN ** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.050189 restraints weight = 93354.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.051775 restraints weight = 46628.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.052823 restraints weight = 29290.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.053585 restraints weight = 21162.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.054053 restraints weight = 16713.785| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.152 21616 Z= 0.290 Angle : 0.805 51.989 29375 Z= 0.408 Chirality : 0.045 0.184 3474 Planarity : 0.004 0.061 3650 Dihedral : 6.873 103.771 2919 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.38 % Allowed : 21.57 % Favored : 73.05 % 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: -0.41 (0.16), residues: 2663 helix: 0.58 (0.14), residues: 1368 sheet: -0.54 (0.32), residues: 239 loop : -1.28 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 75 TYR 0.026 0.002 TYR C 268 PHE 0.028 0.002 PHE E 133 TRP 0.020 0.002 TRP A 83 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00625 (21611) covalent geometry : angle 0.72402 (29365) SS BOND : bond 0.01972 ( 5) SS BOND : angle 19.05058 ( 10) hydrogen bonds : bond 0.04495 ( 1148) hydrogen bonds : angle 4.60277 ( 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 415 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 291 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 ASN cc_start: 0.9138 (m-40) cc_final: 0.8830 (m110) REVERT: B 163 MET cc_start: 0.9452 (mmm) cc_final: 0.9190 (mmm) REVERT: B 185 LYS cc_start: 0.9362 (ttmm) cc_final: 0.8974 (tptp) REVERT: B 240 MET cc_start: 0.9241 (tmm) cc_final: 0.8345 (tmm) REVERT: B 242 ASN cc_start: 0.8640 (p0) cc_final: 0.8367 (p0) REVERT: B 296 ILE cc_start: 0.9365 (mp) cc_final: 0.8866 (tt) REVERT: C 39 LYS cc_start: 0.9437 (mmmm) cc_final: 0.8806 (tmtt) REVERT: C 47 LYS cc_start: 0.8283 (tppt) cc_final: 0.8050 (tppt) REVERT: C 65 ASP cc_start: 0.8728 (t0) cc_final: 0.8203 (t0) REVERT: C 84 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9108 (tt) REVERT: C 144 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9207 (tp) REVERT: C 160 ASN cc_start: 0.9216 (m-40) cc_final: 0.8860 (m110) REVERT: C 169 MET cc_start: 0.9093 (ttm) cc_final: 0.8827 (ttm) REVERT: C 170 LYS cc_start: 0.9531 (tptm) cc_final: 0.9277 (tttm) REVERT: C 179 GLU cc_start: 0.8597 (mp0) cc_final: 0.8328 (mp0) REVERT: C 204 ASP cc_start: 0.8464 (t0) cc_final: 0.8186 (t0) REVERT: C 214 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.8764 (t) REVERT: C 240 MET cc_start: 0.8318 (tmm) cc_final: 0.8114 (tmm) REVERT: C 247 ASN cc_start: 0.8903 (p0) cc_final: 0.8596 (p0) REVERT: D 55 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8693 (t80) REVERT: D 56 LEU cc_start: 0.9370 (tp) cc_final: 0.9087 (tt) REVERT: D 77 MET cc_start: 0.8825 (ttp) cc_final: 0.8591 (tpp) REVERT: D 88 MET cc_start: 0.8694 (tmm) cc_final: 0.7927 (tmm) REVERT: D 163 MET cc_start: 0.9178 (mmm) cc_final: 0.8782 (mmm) REVERT: D 170 LYS cc_start: 0.9399 (tptp) cc_final: 0.8927 (tptt) REVERT: D 262 ASP cc_start: 0.9062 (t0) cc_final: 0.8796 (t70) REVERT: D 288 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7751 (tt0) REVERT: D 292 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8209 (tm-30) REVERT: E 30 ASP cc_start: 0.8933 (m-30) cc_final: 0.8701 (m-30) REVERT: E 45 PHE cc_start: 0.9095 (m-80) cc_final: 0.8894 (t80) REVERT: E 86 LEU cc_start: 0.9867 (mt) cc_final: 0.9593 (tp) REVERT: E 108 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: E 271 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8342 (m-10) REVERT: E 442 MET cc_start: 0.8799 (tpt) cc_final: 0.8534 (tpt) REVERT: E 486 GLN cc_start: 0.9726 (OUTLIER) cc_final: 0.9485 (mm110) REVERT: E 503 MET cc_start: 0.9160 (mmm) cc_final: 0.8783 (tpt) REVERT: E 507 ILE cc_start: 0.9671 (OUTLIER) cc_final: 0.9264 (tp) REVERT: E 584 PHE cc_start: 0.9086 (m-80) cc_final: 0.8839 (m-80) REVERT: E 611 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9269 (mm) REVERT: E 711 MET cc_start: 0.8135 (mpp) cc_final: 0.7748 (mpp) REVERT: E 790 PHE cc_start: 0.8716 (t80) cc_final: 0.8505 (t80) REVERT: E 1066 MET cc_start: 0.7914 (mmm) cc_final: 0.7650 (mmt) REVERT: E 1110 MET cc_start: 0.8625 (mtp) cc_final: 0.8276 (mmt) REVERT: E 1129 CYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8147 (p) REVERT: E 1191 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8897 (tp-100) REVERT: E 1239 LEU cc_start: 0.9764 (OUTLIER) cc_final: 0.9528 (tp) REVERT: E 1287 TYR cc_start: 0.8945 (m-80) cc_final: 0.8608 (m-80) REVERT: E 1525 MET cc_start: 0.8576 (ptp) cc_final: 0.8217 (ppp) outliers start: 124 outliers final: 80 residues processed: 393 average time/residue: 0.1352 time to fit residues: 87.2698 Evaluate side-chains 357 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 266 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 196 LEU 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 341 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 259 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS 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 131 ILE Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 146 ILE 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 339 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL 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 251 LEU 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 108 TYR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 271 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 507 ILE Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 702 ILE 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 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 1175 CYS Chi-restraints excluded: chain E residue 1198 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 150 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 65 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN E 11 ASN ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1234 ASN ** 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 = 0.3182 r_free = 0.3182 target = 0.063619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.052694 restraints weight = 92068.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054338 restraints weight = 46016.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.055468 restraints weight = 28589.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.056171 restraints weight = 20412.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.056717 restraints weight = 16218.218| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 21616 Z= 0.160 Angle : 0.745 52.206 29375 Z= 0.368 Chirality : 0.044 0.161 3474 Planarity : 0.004 0.063 3650 Dihedral : 6.620 105.342 2919 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.77 % Allowed : 22.92 % Favored : 72.31 % 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: 0.64 (0.14), residues: 1393 sheet: -0.32 (0.33), residues: 239 loop : -1.23 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1539 TYR 0.012 0.001 TYR E 379 PHE 0.029 0.001 PHE E 133 TRP 0.012 0.001 TRP B 83 HIS 0.006 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00358 (21611) covalent geometry : angle 0.65645 (29365) SS BOND : bond 0.01846 ( 5) SS BOND : angle 19.05555 ( 10) hydrogen bonds : bond 0.04090 ( 1148) hydrogen bonds : angle 4.37423 ( 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 427 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 317 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9326 (mt) cc_final: 0.8885 (pp) REVERT: A 83 TRP cc_start: 0.9685 (m-10) cc_final: 0.9093 (m-90) REVERT: B 160 ASN cc_start: 0.9139 (m-40) cc_final: 0.8837 (m110) REVERT: B 185 LYS cc_start: 0.9343 (ttmm) cc_final: 0.8855 (tptt) REVERT: B 240 MET cc_start: 0.9247 (tmm) cc_final: 0.8482 (tmm) REVERT: B 296 ILE cc_start: 0.9297 (mp) cc_final: 0.8851 (tt) REVERT: B 332 LYS cc_start: 0.8993 (mmtm) cc_final: 0.8776 (mmtm) REVERT: C 39 LYS cc_start: 0.9277 (mmmm) cc_final: 0.8748 (tmtt) REVERT: C 47 LYS cc_start: 0.8741 (tppt) cc_final: 0.8385 (tppt) REVERT: C 65 ASP cc_start: 0.8448 (t0) cc_final: 0.7993 (t0) REVERT: C 84 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9152 (tt) REVERT: C 160 ASN cc_start: 0.9201 (m-40) cc_final: 0.8849 (m110) REVERT: C 169 MET cc_start: 0.9028 (ttm) cc_final: 0.8730 (ttm) REVERT: C 170 LYS cc_start: 0.9483 (tptm) cc_final: 0.9230 (tttp) REVERT: C 179 GLU cc_start: 0.8575 (mp0) cc_final: 0.7957 (mp0) REVERT: C 199 MET cc_start: 0.8870 (mtm) cc_final: 0.8285 (mpp) REVERT: C 214 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.8587 (t) REVERT: C 240 MET cc_start: 0.7940 (tmm) cc_final: 0.7212 (tmm) REVERT: C 247 ASN cc_start: 0.8795 (p0) cc_final: 0.8463 (p0) REVERT: D 56 LEU cc_start: 0.9368 (tp) cc_final: 0.9037 (tt) REVERT: D 77 MET cc_start: 0.8738 (ttp) cc_final: 0.8388 (tpp) REVERT: D 88 MET cc_start: 0.8624 (tmm) cc_final: 0.7904 (tmm) REVERT: D 163 MET cc_start: 0.9250 (mmm) cc_final: 0.8888 (mmm) REVERT: D 170 LYS cc_start: 0.9250 (tptp) cc_final: 0.8653 (tptt) REVERT: D 240 MET cc_start: 0.8636 (tmm) cc_final: 0.8265 (tmm) REVERT: D 262 ASP cc_start: 0.9026 (t0) cc_final: 0.8780 (t70) REVERT: D 288 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7700 (tt0) REVERT: D 292 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8135 (tm-30) REVERT: E 30 ASP cc_start: 0.8904 (m-30) cc_final: 0.8611 (m-30) REVERT: E 86 LEU cc_start: 0.9871 (mt) cc_final: 0.9631 (tp) REVERT: E 108 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: E 251 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8945 (tp) REVERT: E 271 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8307 (m-10) REVERT: E 419 CYS cc_start: 0.9187 (m) cc_final: 0.8771 (t) REVERT: E 445 GLN cc_start: 0.8987 (tt0) cc_final: 0.8565 (tp40) REVERT: E 486 GLN cc_start: 0.9693 (OUTLIER) cc_final: 0.9434 (mm110) REVERT: E 503 MET cc_start: 0.9019 (mmm) cc_final: 0.8630 (tpt) REVERT: E 584 PHE cc_start: 0.9018 (m-80) cc_final: 0.8610 (m-80) REVERT: E 611 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9249 (mm) REVERT: E 711 MET cc_start: 0.8278 (mpp) cc_final: 0.7802 (mpp) REVERT: E 1066 MET cc_start: 0.8109 (mmm) cc_final: 0.7829 (mmt) REVERT: E 1129 CYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8139 (p) REVERT: E 1143 LEU cc_start: 0.9518 (tt) cc_final: 0.9217 (pp) REVERT: E 1280 LEU cc_start: 0.9385 (mm) cc_final: 0.9169 (mm) REVERT: E 1525 MET cc_start: 0.8506 (ptp) cc_final: 0.8106 (ppp) outliers start: 110 outliers final: 72 residues processed: 409 average time/residue: 0.1348 time to fit residues: 90.7061 Evaluate side-chains 361 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 281 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 296 ILE 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 345 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 345 THR 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 131 ILE 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 80 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 181 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 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 12 HIS 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 237 PHE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 271 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 486 GLN Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 702 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 884 VAL 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 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 1375 ILE 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: chunk 219 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 153 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN E 60 HIS ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.053444 restraints weight = 91319.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.055105 restraints weight = 45356.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.056241 restraints weight = 28078.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.057005 restraints weight = 19953.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.057530 restraints weight = 15659.549| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 21616 Z= 0.149 Angle : 0.747 52.207 29375 Z= 0.367 Chirality : 0.044 0.191 3474 Planarity : 0.004 0.063 3650 Dihedral : 6.508 106.688 2918 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.17 % Allowed : 24.00 % Favored : 71.83 % 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: -0.15 (0.16), residues: 2663 helix: 0.70 (0.14), residues: 1395 sheet: -0.10 (0.33), residues: 238 loop : -1.15 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1539 TYR 0.011 0.001 TYR E 231 PHE 0.026 0.001 PHE E 133 TRP 0.017 0.001 TRP B 83 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00339 (21611) covalent geometry : angle 0.65978 (29365) SS BOND : bond 0.01830 ( 5) SS BOND : angle 19.03100 ( 10) hydrogen bonds : bond 0.04007 ( 1148) hydrogen bonds : angle 4.29785 ( 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 403 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 307 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9262 (mt) cc_final: 0.8798 (pp) REVERT: A 83 TRP cc_start: 0.9665 (m-10) cc_final: 0.9081 (m-90) REVERT: B 148 ILE cc_start: 0.9701 (tt) cc_final: 0.9446 (tp) REVERT: B 160 ASN cc_start: 0.9135 (m-40) cc_final: 0.8811 (m110) REVERT: B 163 MET cc_start: 0.9416 (mmm) cc_final: 0.9128 (mmm) REVERT: B 185 LYS cc_start: 0.9349 (ttmm) cc_final: 0.8871 (tptt) REVERT: B 240 MET cc_start: 0.9174 (tmm) cc_final: 0.8329 (tmm) REVERT: B 296 ILE cc_start: 0.9278 (mp) cc_final: 0.8857 (tt) REVERT: B 332 LYS cc_start: 0.9014 (mmtm) cc_final: 0.8697 (mmtm) REVERT: C 39 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8718 (tmtt) REVERT: C 47 LYS cc_start: 0.8698 (tppt) cc_final: 0.8373 (tppt) REVERT: C 65 ASP cc_start: 0.8431 (t0) cc_final: 0.7995 (t0) REVERT: C 84 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9156 (tt) REVERT: C 160 ASN cc_start: 0.9196 (m-40) cc_final: 0.8839 (m110) REVERT: C 169 MET cc_start: 0.8988 (ttm) cc_final: 0.8694 (ttm) REVERT: C 170 LYS cc_start: 0.9460 (tptm) cc_final: 0.9223 (tttm) REVERT: C 179 GLU cc_start: 0.8554 (mp0) cc_final: 0.8246 (mp0) REVERT: C 199 MET cc_start: 0.8918 (mtm) cc_final: 0.8267 (mpp) REVERT: C 214 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.8512 (t) REVERT: C 240 MET cc_start: 0.7806 (tmm) cc_final: 0.7043 (tmm) REVERT: C 247 ASN cc_start: 0.8706 (p0) cc_final: 0.8354 (p0) REVERT: C 338 LYS cc_start: 0.9187 (tppt) cc_final: 0.8981 (tppt) REVERT: D 56 LEU cc_start: 0.9369 (tp) cc_final: 0.9040 (tt) REVERT: D 77 MET cc_start: 0.8734 (ttp) cc_final: 0.8333 (tpp) REVERT: D 88 MET cc_start: 0.8575 (tmm) cc_final: 0.7839 (tmm) REVERT: D 163 MET cc_start: 0.9256 (mmm) cc_final: 0.8901 (mmm) REVERT: D 170 LYS cc_start: 0.9238 (tptp) cc_final: 0.8677 (tptt) REVERT: D 240 MET cc_start: 0.8660 (tmm) cc_final: 0.8330 (tmm) REVERT: D 262 ASP cc_start: 0.9021 (t0) cc_final: 0.8766 (t70) REVERT: D 288 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7690 (tt0) REVERT: D 292 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8094 (tm-30) REVERT: E 30 ASP cc_start: 0.8899 (m-30) cc_final: 0.8584 (m-30) REVERT: E 86 LEU cc_start: 0.9872 (mt) cc_final: 0.9623 (tp) REVERT: E 108 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: E 116 MET cc_start: 0.9256 (mmm) cc_final: 0.9047 (tpp) REVERT: E 153 ILE cc_start: 0.9634 (mm) cc_final: 0.9321 (mm) REVERT: E 211 LEU cc_start: 0.8448 (pt) cc_final: 0.8223 (pp) REVERT: E 251 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8941 (tp) REVERT: E 271 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8265 (m-10) REVERT: E 419 CYS cc_start: 0.9234 (m) cc_final: 0.8890 (t) REVERT: E 486 GLN cc_start: 0.9678 (OUTLIER) cc_final: 0.9459 (mm110) REVERT: E 503 MET cc_start: 0.8999 (mmm) cc_final: 0.8615 (tpt) REVERT: E 507 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9154 (tp) REVERT: E 584 PHE cc_start: 0.8971 (m-80) cc_final: 0.8522 (m-80) REVERT: E 611 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9245 (mm) REVERT: E 711 MET cc_start: 0.8263 (mpp) cc_final: 0.7781 (mpp) REVERT: E 869 MET cc_start: 0.8364 (tpt) cc_final: 0.7912 (mmm) REVERT: E 1066 MET cc_start: 0.8249 (mmm) cc_final: 0.7945 (mmt) REVERT: E 1080 LEU cc_start: 0.9268 (mm) cc_final: 0.8984 (mm) REVERT: E 1110 MET cc_start: 0.8620 (mtp) cc_final: 0.8240 (mmt) REVERT: E 1129 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8169 (p) REVERT: E 1143 LEU cc_start: 0.9552 (tt) cc_final: 0.9237 (pp) REVERT: E 1226 LYS cc_start: 0.8758 (mmtp) cc_final: 0.8486 (mmtp) REVERT: E 1287 TYR cc_start: 0.8817 (m-80) cc_final: 0.8615 (m-80) REVERT: E 1395 MET cc_start: 0.9057 (tmm) cc_final: 0.8781 (tpt) REVERT: E 1505 MET cc_start: 0.8906 (mpp) cc_final: 0.8404 (mmm) REVERT: E 1525 MET cc_start: 0.8495 (ptp) cc_final: 0.8038 (ppp) outliers start: 96 outliers final: 70 residues processed: 384 average time/residue: 0.1351 time to fit residues: 84.6077 Evaluate side-chains 373 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 294 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 HIS 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 296 ILE 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 345 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 345 THR 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 131 ILE 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 138 VAL 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 259 HIS 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 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 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 251 ILE Chi-restraints excluded: chain E residue 271 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 486 GLN Chi-restraints excluded: chain E residue 507 ILE 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 884 VAL 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 1129 CYS 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 1375 ILE 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: chunk 208 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN D 279 GLN ** 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 = 0.3146 r_free = 0.3146 target = 0.061755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.051090 restraints weight = 92986.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.052680 restraints weight = 46806.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.053754 restraints weight = 29695.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.054506 restraints weight = 21513.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.054977 restraints weight = 17042.305| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 21616 Z= 0.214 Angle : 0.781 52.261 29375 Z= 0.387 Chirality : 0.044 0.198 3474 Planarity : 0.004 0.061 3650 Dihedral : 6.590 112.167 2918 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.64 % Allowed : 24.09 % Favored : 71.27 % 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: -0.15 (0.16), residues: 2663 helix: 0.69 (0.14), residues: 1395 sheet: -0.15 (0.33), residues: 239 loop : -1.12 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 75 TYR 0.014 0.001 TYR C 268 PHE 0.028 0.002 PHE E 133 TRP 0.018 0.001 TRP B 83 HIS 0.004 0.001 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00472 (21611) covalent geometry : angle 0.69819 (29365) SS BOND : bond 0.01868 ( 5) SS BOND : angle 19.02780 ( 10) hydrogen bonds : bond 0.04154 ( 1148) hydrogen bonds : angle 4.39310 ( 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 404 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 297 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9384 (mt) cc_final: 0.8978 (pp) REVERT: A 83 TRP cc_start: 0.9676 (m-10) cc_final: 0.9116 (m-90) REVERT: B 77 MET cc_start: 0.8983 (tpp) cc_final: 0.8728 (mmm) REVERT: B 148 ILE cc_start: 0.9710 (tt) cc_final: 0.9477 (tp) REVERT: B 160 ASN cc_start: 0.9127 (m-40) cc_final: 0.8833 (m110) REVERT: B 163 MET cc_start: 0.9488 (mmm) cc_final: 0.9239 (mmm) REVERT: B 185 LYS cc_start: 0.9341 (ttmm) cc_final: 0.8865 (tptp) REVERT: B 240 MET cc_start: 0.9104 (tmm) cc_final: 0.8211 (tmm) REVERT: B 349 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9064 (mm) REVERT: C 39 LYS cc_start: 0.9270 (mmmm) cc_final: 0.8753 (tmtt) REVERT: C 47 LYS cc_start: 0.8759 (tppt) cc_final: 0.8402 (tppt) REVERT: C 65 ASP cc_start: 0.8566 (t0) cc_final: 0.8102 (t0) REVERT: C 84 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9100 (tt) REVERT: C 144 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9164 (tp) REVERT: C 160 ASN cc_start: 0.9169 (m-40) cc_final: 0.8817 (m110) REVERT: C 169 MET cc_start: 0.9081 (ttm) cc_final: 0.8809 (ttm) REVERT: C 170 LYS cc_start: 0.9504 (tptm) cc_final: 0.9150 (tttp) REVERT: C 179 GLU cc_start: 0.8607 (mp0) cc_final: 0.7892 (mp0) REVERT: C 199 MET cc_start: 0.9006 (mtm) cc_final: 0.8314 (mpp) REVERT: C 214 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.8783 (t) REVERT: C 247 ASN cc_start: 0.8790 (p0) cc_final: 0.8327 (p0) REVERT: C 338 LYS cc_start: 0.9271 (tppt) cc_final: 0.9066 (tppt) REVERT: D 56 LEU cc_start: 0.9424 (tp) cc_final: 0.9062 (tt) REVERT: D 77 MET cc_start: 0.8756 (ttp) cc_final: 0.8358 (tpp) REVERT: D 88 MET cc_start: 0.8647 (tmm) cc_final: 0.7854 (tmm) REVERT: D 163 MET cc_start: 0.9240 (mmm) cc_final: 0.8888 (mmm) REVERT: D 170 LYS cc_start: 0.9296 (tptp) cc_final: 0.8756 (tptt) REVERT: D 240 MET cc_start: 0.8726 (tmm) cc_final: 0.8338 (tmm) REVERT: D 262 ASP cc_start: 0.8978 (t0) cc_final: 0.8633 (t70) REVERT: D 288 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7713 (tt0) REVERT: D 292 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8262 (tm-30) REVERT: E 30 ASP cc_start: 0.8956 (m-30) cc_final: 0.8665 (m-30) REVERT: E 83 LEU cc_start: 0.9650 (mt) cc_final: 0.9422 (mt) REVERT: E 86 LEU cc_start: 0.9872 (mt) cc_final: 0.9640 (tp) REVERT: E 108 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: E 211 LEU cc_start: 0.8442 (pt) cc_final: 0.8204 (pp) REVERT: E 251 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9071 (tp) REVERT: E 271 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8266 (m-10) REVERT: E 419 CYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8772 (t) REVERT: E 503 MET cc_start: 0.9049 (mmm) cc_final: 0.8633 (tpt) REVERT: E 507 ILE cc_start: 0.9642 (OUTLIER) cc_final: 0.9410 (tp) REVERT: E 584 PHE cc_start: 0.9053 (m-80) cc_final: 0.8601 (m-80) REVERT: E 611 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9221 (mm) REVERT: E 711 MET cc_start: 0.8247 (mpp) cc_final: 0.7805 (mpp) REVERT: E 1066 MET cc_start: 0.8422 (mmm) cc_final: 0.8102 (mmt) REVERT: E 1110 MET cc_start: 0.8614 (mtp) cc_final: 0.8275 (mmm) REVERT: E 1129 CYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8204 (p) REVERT: E 1143 LEU cc_start: 0.9561 (tt) cc_final: 0.9295 (pp) REVERT: E 1191 GLN cc_start: 0.9216 (tp40) cc_final: 0.8791 (tp-100) REVERT: E 1226 LYS cc_start: 0.8765 (mmtp) cc_final: 0.8563 (mmtp) REVERT: E 1280 LEU cc_start: 0.8950 (mm) cc_final: 0.8665 (tp) REVERT: E 1395 MET cc_start: 0.9075 (tmm) cc_final: 0.8820 (tpt) REVERT: E 1505 MET cc_start: 0.8969 (mpp) cc_final: 0.8345 (mmm) REVERT: E 1525 MET cc_start: 0.8588 (ptp) cc_final: 0.8097 (ppp) outliers start: 107 outliers final: 81 residues processed: 384 average time/residue: 0.1346 time to fit residues: 84.6630 Evaluate side-chains 375 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 283 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 196 LEU 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 251 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 345 THR 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 80 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 146 ILE 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 C residue 339 VAL Chi-restraints excluded: chain D residue 138 VAL 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 251 LEU Chi-restraints excluded: chain D residue 259 HIS 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 12 HIS 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 190 VAL Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 251 ILE 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 359 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 419 CYS 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 507 ILE 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 884 VAL 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 1129 CYS 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 1281 VAL Chi-restraints excluded: chain E residue 1375 ILE Chi-restraints excluded: chain E residue 1497 VAL Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 108 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 258 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 208 optimal weight: 0.0980 chunk 179 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 335 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.064785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.053821 restraints weight = 90191.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.055500 restraints weight = 44704.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.056664 restraints weight = 27672.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.057457 restraints weight = 19598.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.057991 restraints weight = 15298.594| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 21616 Z= 0.134 Angle : 0.756 52.300 29375 Z= 0.367 Chirality : 0.044 0.278 3474 Planarity : 0.004 0.063 3650 Dihedral : 6.389 110.011 2917 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.52 % Allowed : 25.74 % Favored : 70.75 % 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: 0.07 (0.16), residues: 2663 helix: 0.93 (0.14), residues: 1371 sheet: 0.04 (0.33), residues: 239 loop : -1.08 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1539 TYR 0.013 0.001 TYR E 231 PHE 0.026 0.001 PHE E 364 TRP 0.015 0.001 TRP B 83 HIS 0.005 0.001 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00305 (21611) covalent geometry : angle 0.66967 (29365) SS BOND : bond 0.01779 ( 5) SS BOND : angle 19.02981 ( 10) hydrogen bonds : bond 0.03872 ( 1148) hydrogen bonds : angle 4.23619 ( 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 421 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 340 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9296 (mt) cc_final: 0.8875 (pp) REVERT: A 77 MET cc_start: 0.8731 (tpp) cc_final: 0.8193 (ttt) REVERT: A 83 TRP cc_start: 0.9673 (m-10) cc_final: 0.9139 (m-90) REVERT: B 39 LYS cc_start: 0.9446 (mmmm) cc_final: 0.9204 (mtmm) REVERT: B 148 ILE cc_start: 0.9660 (tt) cc_final: 0.9451 (tp) REVERT: B 160 ASN cc_start: 0.9129 (m-40) cc_final: 0.8862 (m110) REVERT: B 163 MET cc_start: 0.9474 (mmm) cc_final: 0.9191 (mmm) REVERT: B 185 LYS cc_start: 0.9339 (ttmm) cc_final: 0.8795 (tptt) REVERT: B 240 MET cc_start: 0.9124 (tmm) cc_final: 0.8295 (tmm) REVERT: B 250 PHE cc_start: 0.8386 (t80) cc_final: 0.8121 (t80) REVERT: B 296 ILE cc_start: 0.9291 (mp) cc_final: 0.8895 (tt) REVERT: B 349 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9054 (mm) REVERT: C 39 LYS cc_start: 0.9263 (mmmm) cc_final: 0.8682 (tmtt) REVERT: C 65 ASP cc_start: 0.8474 (t0) cc_final: 0.8050 (t0) REVERT: C 84 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9103 (tt) REVERT: C 144 LEU cc_start: 0.9388 (mm) cc_final: 0.9096 (tp) REVERT: C 160 ASN cc_start: 0.9137 (m-40) cc_final: 0.8795 (m110) REVERT: C 169 MET cc_start: 0.9023 (ttm) cc_final: 0.8652 (ttm) REVERT: C 179 GLU cc_start: 0.8569 (mp0) cc_final: 0.7905 (mp0) REVERT: C 199 MET cc_start: 0.8963 (mtm) cc_final: 0.8123 (mpp) REVERT: C 214 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8794 (t) REVERT: C 240 MET cc_start: 0.7487 (tmm) cc_final: 0.7206 (tmm) REVERT: C 338 LYS cc_start: 0.9253 (tppt) cc_final: 0.8704 (tptp) REVERT: D 50 ARG cc_start: 0.7287 (mmp-170) cc_final: 0.6790 (mmp80) REVERT: D 56 LEU cc_start: 0.9392 (tp) cc_final: 0.9040 (tt) REVERT: D 77 MET cc_start: 0.8620 (ttp) cc_final: 0.7849 (tpp) REVERT: D 88 MET cc_start: 0.8564 (tmm) cc_final: 0.7818 (tmm) REVERT: D 163 MET cc_start: 0.9292 (mmm) cc_final: 0.8955 (mmm) REVERT: D 170 LYS cc_start: 0.9201 (tptp) cc_final: 0.8640 (tptt) REVERT: D 240 MET cc_start: 0.8643 (tmm) cc_final: 0.8332 (tmm) REVERT: D 262 ASP cc_start: 0.8979 (t0) cc_final: 0.8667 (t70) REVERT: D 288 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7677 (tt0) REVERT: D 292 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8139 (tm-30) REVERT: E 30 ASP cc_start: 0.8932 (m-30) cc_final: 0.8618 (m-30) REVERT: E 80 PHE cc_start: 0.8810 (m-80) cc_final: 0.8597 (m-80) REVERT: E 105 LEU cc_start: 0.9445 (mt) cc_final: 0.9208 (mt) REVERT: E 108 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: E 153 ILE cc_start: 0.9635 (mm) cc_final: 0.9297 (mm) REVERT: E 175 LEU cc_start: 0.9065 (tt) cc_final: 0.8856 (tt) REVERT: E 251 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8913 (tp) REVERT: E 271 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8251 (m-10) REVERT: E 503 MET cc_start: 0.8994 (mmm) cc_final: 0.8647 (tpt) REVERT: E 507 ILE cc_start: 0.9605 (OUTLIER) cc_final: 0.9119 (tp) REVERT: E 584 PHE cc_start: 0.9008 (m-80) cc_final: 0.8678 (m-80) REVERT: E 611 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9196 (mm) REVERT: E 869 MET cc_start: 0.8323 (tpt) cc_final: 0.7821 (mmm) REVERT: E 1066 MET cc_start: 0.8387 (mmm) cc_final: 0.8051 (mmt) REVERT: E 1110 MET cc_start: 0.8615 (mtp) cc_final: 0.8209 (mmt) REVERT: E 1141 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8958 (tm-30) REVERT: E 1143 LEU cc_start: 0.9542 (tt) cc_final: 0.9254 (pp) REVERT: E 1154 LEU cc_start: 0.9316 (mm) cc_final: 0.9003 (tp) REVERT: E 1188 ASP cc_start: 0.8734 (t70) cc_final: 0.8294 (t0) REVERT: E 1226 LYS cc_start: 0.8757 (mmtp) cc_final: 0.8459 (mmtp) REVERT: E 1280 LEU cc_start: 0.8880 (mm) cc_final: 0.8581 (tp) REVERT: E 1287 TYR cc_start: 0.8740 (m-80) cc_final: 0.8459 (m-80) REVERT: E 1395 MET cc_start: 0.9109 (tmm) cc_final: 0.8819 (tpt) REVERT: E 1505 MET cc_start: 0.8889 (mpp) cc_final: 0.8351 (mmm) REVERT: E 1525 MET cc_start: 0.8375 (ptp) cc_final: 0.7838 (ppp) outliers start: 81 outliers final: 63 residues processed: 403 average time/residue: 0.1332 time to fit residues: 87.5120 Evaluate side-chains 380 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 309 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 HIS 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 296 ILE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 345 THR 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 139 THR Chi-restraints excluded: chain C residue 146 ILE 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 138 VAL 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 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 108 TYR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 251 ILE 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 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 507 ILE 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 884 VAL 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 1136 ILE 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 1281 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: chunk 100 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 127 optimal weight: 0.0020 chunk 65 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3214 r_free = 0.3214 target = 0.065081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.054048 restraints weight = 90527.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.055744 restraints weight = 44853.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.056891 restraints weight = 27789.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.057697 restraints weight = 19779.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.058245 restraints weight = 15414.334| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 21616 Z= 0.137 Angle : 0.766 52.268 29375 Z= 0.372 Chirality : 0.043 0.218 3474 Planarity : 0.004 0.063 3650 Dihedral : 6.333 109.618 2917 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.43 % Allowed : 26.35 % Favored : 70.23 % 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: 0.14 (0.16), residues: 2663 helix: 0.97 (0.14), residues: 1367 sheet: 0.35 (0.34), residues: 231 loop : -1.09 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1539 TYR 0.013 0.001 TYR E 231 PHE 0.026 0.001 PHE E 133 TRP 0.018 0.001 TRP B 83 HIS 0.004 0.001 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00313 (21611) covalent geometry : angle 0.68148 (29365) SS BOND : bond 0.01800 ( 5) SS BOND : angle 19.01874 ( 10) hydrogen bonds : bond 0.03857 ( 1148) hydrogen bonds : angle 4.20870 ( 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 408 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 329 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9289 (mt) cc_final: 0.8869 (pp) REVERT: A 77 MET cc_start: 0.8809 (tpp) cc_final: 0.8246 (ttt) REVERT: A 83 TRP cc_start: 0.9656 (m-10) cc_final: 0.9125 (m-90) REVERT: B 39 LYS cc_start: 0.9400 (mmmm) cc_final: 0.9111 (mtmm) REVERT: B 148 ILE cc_start: 0.9641 (tt) cc_final: 0.9434 (tp) REVERT: B 160 ASN cc_start: 0.9144 (m-40) cc_final: 0.8848 (m110) REVERT: B 163 MET cc_start: 0.9459 (mmm) cc_final: 0.9177 (mmm) REVERT: B 169 MET cc_start: 0.9020 (ttm) cc_final: 0.8761 (ttm) REVERT: B 185 LYS cc_start: 0.9329 (ttmm) cc_final: 0.8774 (tptt) REVERT: B 240 MET cc_start: 0.9065 (tmm) cc_final: 0.8240 (tmm) REVERT: B 250 PHE cc_start: 0.8422 (t80) cc_final: 0.8180 (t80) REVERT: B 296 ILE cc_start: 0.9277 (mp) cc_final: 0.8902 (tt) REVERT: B 349 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9063 (mm) REVERT: C 39 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8666 (tmtt) REVERT: C 65 ASP cc_start: 0.8442 (t0) cc_final: 0.7999 (t0) REVERT: C 84 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9090 (tt) REVERT: C 144 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9157 (tp) REVERT: C 160 ASN cc_start: 0.9132 (m-40) cc_final: 0.8785 (m110) REVERT: C 169 MET cc_start: 0.8996 (ttm) cc_final: 0.8663 (ttm) REVERT: C 179 GLU cc_start: 0.8561 (mp0) cc_final: 0.7893 (mp0) REVERT: C 199 MET cc_start: 0.8970 (mtm) cc_final: 0.8142 (mpp) REVERT: C 207 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8546 (ttmt) REVERT: C 214 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8732 (t) REVERT: C 240 MET cc_start: 0.7568 (tmm) cc_final: 0.7263 (tmm) REVERT: C 338 LYS cc_start: 0.9284 (tppt) cc_final: 0.8752 (tptp) REVERT: D 50 ARG cc_start: 0.7255 (mmp-170) cc_final: 0.6778 (mmp80) REVERT: D 56 LEU cc_start: 0.9414 (tp) cc_final: 0.9045 (tt) REVERT: D 77 MET cc_start: 0.8557 (ttp) cc_final: 0.7804 (tpp) REVERT: D 88 MET cc_start: 0.8573 (tmm) cc_final: 0.7844 (tmm) REVERT: D 163 MET cc_start: 0.9280 (mmm) cc_final: 0.8942 (mmm) REVERT: D 170 LYS cc_start: 0.9203 (tptp) cc_final: 0.8631 (tptt) REVERT: D 240 MET cc_start: 0.8594 (tmm) cc_final: 0.8265 (tmm) REVERT: D 262 ASP cc_start: 0.8964 (t0) cc_final: 0.8660 (t70) REVERT: D 288 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7711 (tt0) REVERT: D 292 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8132 (tm-30) REVERT: D 332 LYS cc_start: 0.9361 (ttpt) cc_final: 0.8737 (ttpp) REVERT: E 30 ASP cc_start: 0.8941 (m-30) cc_final: 0.8631 (m-30) REVERT: E 62 HIS cc_start: 0.8393 (t-90) cc_final: 0.8057 (t-90) REVERT: E 80 PHE cc_start: 0.8891 (m-80) cc_final: 0.8577 (m-80) REVERT: E 83 LEU cc_start: 0.9562 (mt) cc_final: 0.9345 (mt) REVERT: E 105 LEU cc_start: 0.9436 (mt) cc_final: 0.9187 (mt) REVERT: E 108 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: E 153 ILE cc_start: 0.9531 (mm) cc_final: 0.9235 (mm) REVERT: E 175 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8858 (tt) REVERT: E 251 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8853 (tp) REVERT: E 271 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8201 (m-10) REVERT: E 315 PHE cc_start: 0.8317 (m-80) cc_final: 0.7956 (m-80) REVERT: E 503 MET cc_start: 0.9011 (mmm) cc_final: 0.8650 (tpt) REVERT: E 507 ILE cc_start: 0.9602 (OUTLIER) cc_final: 0.9136 (tp) REVERT: E 584 PHE cc_start: 0.8992 (m-80) cc_final: 0.8676 (m-80) REVERT: E 611 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9202 (mm) REVERT: E 711 MET cc_start: 0.8241 (mpp) cc_final: 0.7948 (mmt) REVERT: E 869 MET cc_start: 0.8275 (tpt) cc_final: 0.7853 (mmm) REVERT: E 1066 MET cc_start: 0.8367 (mmm) cc_final: 0.8001 (mmt) REVERT: E 1110 MET cc_start: 0.8633 (mtp) cc_final: 0.8244 (mmt) REVERT: E 1141 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8973 (tm-30) REVERT: E 1143 LEU cc_start: 0.9543 (tt) cc_final: 0.9251 (pp) REVERT: E 1154 LEU cc_start: 0.9299 (mm) cc_final: 0.9003 (tp) REVERT: E 1188 ASP cc_start: 0.8701 (t70) cc_final: 0.8249 (t0) REVERT: E 1280 LEU cc_start: 0.8885 (mm) cc_final: 0.8626 (tp) REVERT: E 1395 MET cc_start: 0.9108 (tmm) cc_final: 0.8807 (tpt) REVERT: E 1505 MET cc_start: 0.8883 (mpp) cc_final: 0.8326 (mmm) REVERT: E 1525 MET cc_start: 0.8388 (ptp) cc_final: 0.7828 (ppp) outliers start: 79 outliers final: 63 residues processed: 390 average time/residue: 0.1318 time to fit residues: 84.0435 Evaluate side-chains 386 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 313 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 HIS 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 296 ILE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 146 ILE 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 138 VAL 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 108 TYR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 237 PHE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 251 ILE 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 507 ILE 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 884 VAL 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 1136 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU 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 1281 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: chunk 186 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 250 optimal weight: 0.6980 chunk 196 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 247 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN C 153 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** E 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1348 GLN E1541 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.051648 restraints weight = 91570.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.053249 restraints weight = 46229.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.054356 restraints weight = 29211.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.055112 restraints weight = 20985.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.055574 restraints weight = 16569.124| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 21616 Z= 0.209 Angle : 0.791 52.213 29375 Z= 0.391 Chirality : 0.045 0.203 3474 Planarity : 0.004 0.061 3650 Dihedral : 6.465 114.714 2916 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.73 % Allowed : 26.26 % Favored : 70.01 % 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: 0.99 (0.14), residues: 1346 sheet: 0.31 (0.33), residues: 229 loop : -0.99 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 75 TYR 0.013 0.001 TYR C 268 PHE 0.028 0.001 PHE E 133 TRP 0.019 0.001 TRP B 83 HIS 0.004 0.001 HIS E 585 Details of bonding type rmsd covalent geometry : bond 0.00463 (21611) covalent geometry : angle 0.70951 (29365) SS BOND : bond 0.01865 ( 5) SS BOND : angle 19.01404 ( 10) hydrogen bonds : bond 0.04080 ( 1148) hydrogen bonds : angle 4.33042 ( 3384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3333.47 seconds wall clock time: 58 minutes 51.79 seconds (3531.79 seconds total)