Starting phenix.real_space_refine on Sun Sep 13 04:31:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w0d_32239/09_2026/7w0d_32239.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0d_32239/09_2026/7w0d_32239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7w0d_32239/09_2026/7w0d_32239.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w0d_32239/09_2026/7w0d_32239.cif" model { file = "/net/cci-nas-00/data/ceres_data/7w0d_32239/09_2026/7w0d_32239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0d_32239/09_2026/7w0d_32239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w0d_32239/09_2026/7w0d_32239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0d_32239/09_2026/7w0d_32239.map" } resolution = 4.18 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= 0.038 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 107 5.49 5 Mg 2 5.21 5 S 102 5.16 5 C 12567 2.51 5 N 3476 2.21 5 O 4068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20322 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "D" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1103 Classifications: {'RNAv2': 52} Modifications used: {'rna3p_pur': 25, 'rna3p_pyr': 27} Link IDs: {'rna3p': 51} Chain: "G" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 117 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "A" Number of atoms: 12490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1544, 12490 Classifications: {'peptide': 1544} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 63, 'TRANS': 1480} Chain breaks: 2 Chain: "F" Number of atoms: 5312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5312 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 22, 'TRANS': 637} Chain: "C" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1100 Classifications: {'RNAv2': 52} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 25, 'rna3p_pyr': 25} Link IDs: {'rna2p': 1, 'rna3p': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.87, per 1000 atoms: 0.19 Number of scatterers: 20322 At special positions: 0 Unit cell: (127.735, 100.672, 204.592, 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 102 16.00 P 107 15.00 Mg 2 11.99 O 4068 8.00 N 3476 7.00 C 12567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 630.7 milliseconds 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4268 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 15 sheets defined 54.5% alpha, 9.2% beta 43 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.610A pdb=" N LEU A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 93 through 97 removed outlier: 4.012A pdb=" N ASP A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 removed outlier: 4.625A pdb=" N GLU A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 125 removed outlier: 3.668A pdb=" N PHE A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.502A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.711A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 4.133A pdb=" N ASN A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.893A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 Processing helix chain 'A' and resid 293 through 314 removed outlier: 3.885A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.580A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.755A pdb=" N TYR A 488 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 534 removed outlier: 3.792A pdb=" N GLN A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 529 " --> pdb=" O HIS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 4.296A pdb=" N PHE A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 552 " --> pdb=" O LYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 582 removed outlier: 3.775A pdb=" N ILE A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 608 through 613 removed outlier: 4.426A pdb=" N GLY A 612 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 613' Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.825A pdb=" N ARG A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 741 through 748 Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.709A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 869 removed outlier: 4.316A pdb=" N GLN A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 930 removed outlier: 3.505A pdb=" N MET A 922 " --> pdb=" O TYR A 918 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 Processing helix chain 'A' and resid 972 through 976 removed outlier: 3.515A pdb=" N CYS A 976 " --> pdb=" O PRO A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.568A pdb=" N ILE A 990 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1016 removed outlier: 3.680A pdb=" N HIS A1004 " --> pdb=" O TYR A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1024 Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 4.020A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 removed outlier: 3.541A pdb=" N LEU A1240 " --> pdb=" O ASN A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.780A pdb=" N ASP A1259 " --> pdb=" O PHE A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 removed outlier: 3.518A pdb=" N LEU A1266 " --> pdb=" O PRO A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 3.574A pdb=" N TRP A1277 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1294 Processing helix chain 'A' and resid 1295 through 1300 removed outlier: 3.853A pdb=" N LYS A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.937A pdb=" N LEU A1310 " --> pdb=" O ASN A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1337 Processing helix chain 'A' and resid 1338 through 1341 Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1362 through 1381 removed outlier: 3.746A pdb=" N ILE A1366 " --> pdb=" O PRO A1362 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A1371 " --> pdb=" O ALA A1367 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1376 " --> pdb=" O ALA A1372 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A1377 " --> pdb=" O LEU A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1393 removed outlier: 4.210A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1406 removed outlier: 3.518A pdb=" N GLN A1406 " --> pdb=" O PRO A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1412 Processing helix chain 'A' and resid 1416 through 1420 Processing helix chain 'A' and resid 1425 through 1430 removed outlier: 4.081A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 removed outlier: 3.739A pdb=" N LEU A1436 " --> pdb=" O ASN A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1454 Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 4.640A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1508 removed outlier: 4.212A pdb=" N ASP A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1530 through 1547 removed outlier: 3.587A pdb=" N GLU A1534 " --> pdb=" O ALA A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 3.840A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A1620 " --> pdb=" O LEU A1616 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 removed outlier: 3.649A pdb=" N THR A1633 " --> pdb=" O ASP A1629 " (cutoff:3.500A) Proline residue: A1643 - end of helix removed outlier: 3.724A pdb=" N ARG A1650 " --> pdb=" O GLN A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1662 Processing helix chain 'A' and resid 1701 through 1722 Processing helix chain 'F' and resid 9 through 22 removed outlier: 4.242A pdb=" N ARG F 14 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 21 " --> pdb=" O ASP F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 45 Processing helix chain 'F' and resid 46 through 49 Processing helix chain 'F' and resid 52 through 56 Processing helix chain 'F' and resid 66 through 81 Processing helix chain 'F' and resid 89 through 97 removed outlier: 5.902A pdb=" N VAL F 94 " --> pdb=" O GLU F 91 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP F 95 " --> pdb=" O GLN F 92 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP F 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP F 97 " --> pdb=" O VAL F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 109 removed outlier: 4.607A pdb=" N GLU F 105 " --> pdb=" O MET F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'F' and resid 140 through 144 Processing helix chain 'F' and resid 148 through 160 removed outlier: 3.949A pdb=" N LEU F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE F 157 " --> pdb=" O PHE F 153 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR F 158 " --> pdb=" O MET F 154 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE F 159 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 removed outlier: 3.626A pdb=" N GLU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 213 Processing helix chain 'F' and resid 232 through 252 removed outlier: 3.999A pdb=" N ARG F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP F 250 " --> pdb=" O TYR F 246 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU F 251 " --> pdb=" O VAL F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 313 removed outlier: 7.439A pdb=" N ILE F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N TYR F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA F 295 " --> pdb=" O TYR F 291 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 304 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL F 305 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU F 306 " --> pdb=" O SER F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 344 removed outlier: 3.550A pdb=" N MET F 322 " --> pdb=" O SER F 318 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 362 Processing helix chain 'F' and resid 364 through 379 removed outlier: 3.523A pdb=" N GLN F 368 " --> pdb=" O THR F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 386 Processing helix chain 'F' and resid 394 through 411 removed outlier: 3.805A pdb=" N CYS F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS F 399 " --> pdb=" O ARG F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 416 Processing helix chain 'F' and resid 445 through 452 Processing helix chain 'F' and resid 484 through 495 removed outlier: 3.576A pdb=" N ALA F 495 " --> pdb=" O SER F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 535 Processing helix chain 'F' and resid 543 through 552 Processing helix chain 'F' and resid 567 through 569 No H-bonds generated for 'chain 'F' and resid 567 through 569' Processing helix chain 'F' and resid 570 through 582 removed outlier: 3.638A pdb=" N THR F 581 " --> pdb=" O ARG F 577 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE F 582 " --> pdb=" O TYR F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 606 Processing helix chain 'F' and resid 607 through 611 Processing helix chain 'F' and resid 637 through 656 removed outlier: 3.937A pdb=" N ILE F 643 " --> pdb=" O LYS F 639 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU F 656 " --> pdb=" O VAL F 652 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.210A pdb=" N THR A 219 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU A 504 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 221 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N THR A 506 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL A 223 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N ALA A 507 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N CYS A 388 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N CYS A 460 " --> pdb=" O CYS A 388 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL A 390 " --> pdb=" O CYS A 460 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN A 422 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 357 through 358 removed outlier: 3.572A pdb=" N ILE G 357 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET F 222 " --> pdb=" O ILE G 357 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR F 219 " --> pdb=" O PHE F 502 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU F 504 " --> pdb=" O THR F 219 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL F 221 " --> pdb=" O LEU F 504 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N THR F 506 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 223 " --> pdb=" O THR F 506 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU F 389 " --> pdb=" O PHE F 477 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 88 removed outlier: 3.742A pdb=" N GLY A 114 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ARG A 59 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A 136 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU A 61 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE A 138 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET A 63 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 24 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 170 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE A 25 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA5, first strand: chain 'A' and resid 594 through 596 removed outlier: 3.508A pdb=" N ILE A 630 " --> pdb=" O ILE A 618 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 703 through 706 removed outlier: 4.014A pdb=" N ARG A 703 " --> pdb=" O ILE A1361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 772 removed outlier: 3.549A pdb=" N ARG A 780 " --> pdb=" O PHE A 730 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 768 through 772 removed outlier: 3.549A pdb=" N ARG A 780 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 830 " --> pdb=" O LEU A 757 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AB1, first strand: chain 'A' and resid 969 through 971 removed outlier: 4.723A pdb=" N VAL A 969 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N MET A 939 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL A 898 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLU A 941 " --> pdb=" O THR A 896 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 883 " --> pdb=" O PHE A 977 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1669 through 1670 removed outlier: 3.655A pdb=" N CYS A1684 " --> pdb=" O VAL A1695 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1674 through 1676 removed outlier: 3.743A pdb=" N ILE A1674 " --> pdb=" O MET A1681 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A1681 " --> pdb=" O ILE A1674 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 85 through 88 removed outlier: 5.693A pdb=" N GLY F 86 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR F 115 " --> pdb=" O GLY F 86 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N TYR F 88 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY F 114 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS F 64 " --> pdb=" O GLY F 114 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG F 59 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL F 136 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU F 61 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILE F 138 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N MET F 63 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG F 167 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY F 24 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR F 172 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE F 25 " --> pdb=" O ILE F 200 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AB6, first strand: chain 'F' and resid 593 through 597 removed outlier: 4.437A pdb=" N VAL F 615 " --> pdb=" O LEU F 597 " (cutoff:3.500A) 833 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3891 1.33 - 1.45: 5494 1.45 - 1.57: 11196 1.57 - 1.70: 211 1.70 - 1.82: 160 Bond restraints: 20952 Sorted by residual: bond pdb=" CA SER F 462 " pdb=" C SER F 462 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.34e-02 5.57e+03 3.11e+00 bond pdb=" CD GLN F 520 " pdb=" OE1 GLN F 520 " ideal model delta sigma weight residual 1.231 1.206 0.025 1.90e-02 2.77e+03 1.72e+00 bond pdb=" CD GLU A 209 " pdb=" OE1 GLU A 209 " ideal model delta sigma weight residual 1.249 1.228 0.021 1.90e-02 2.77e+03 1.21e+00 bond pdb=" CA GLU F 140 " pdb=" CB GLU F 140 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.70e-02 3.46e+03 1.17e+00 bond pdb=" N GLU A 499 " pdb=" CA GLU A 499 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.15e+00 ... (remaining 20947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 28373 2.46 - 4.92: 431 4.92 - 7.38: 27 7.38 - 9.84: 6 9.84 - 12.30: 2 Bond angle restraints: 28839 Sorted by residual: angle pdb=" C LYS F 164 " pdb=" N LEU F 165 " pdb=" CA LEU F 165 " ideal model delta sigma weight residual 120.94 133.24 -12.30 1.90e+00 2.77e-01 4.19e+01 angle pdb=" N GLN F 520 " pdb=" CA GLN F 520 " pdb=" CB GLN F 520 " ideal model delta sigma weight residual 110.28 116.73 -6.45 1.55e+00 4.16e-01 1.73e+01 angle pdb=" C LYS A 164 " pdb=" N LEU A 165 " pdb=" CA LEU A 165 " ideal model delta sigma weight residual 120.69 131.59 -10.90 2.95e+00 1.15e-01 1.37e+01 angle pdb=" C TYR F 519 " pdb=" N GLN F 520 " pdb=" CA GLN F 520 " ideal model delta sigma weight residual 120.31 115.31 5.00 1.52e+00 4.33e-01 1.08e+01 angle pdb=" N ASP F 636 " pdb=" CA ASP F 636 " pdb=" C ASP F 636 " ideal model delta sigma weight residual 111.03 114.68 -3.65 1.11e+00 8.12e-01 1.08e+01 ... (remaining 28834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.75: 11194 18.75 - 37.51: 1023 37.51 - 56.26: 186 56.26 - 75.02: 48 75.02 - 93.77: 13 Dihedral angle restraints: 12464 sinusoidal: 5887 harmonic: 6577 Sorted by residual: dihedral pdb=" C4' U C 52 " pdb=" C3' U C 52 " pdb=" C2' U C 52 " pdb=" C1' U C 52 " ideal model delta sinusoidal sigma weight residual 36.35 -35.34 71.69 1 3.10e+00 1.04e-01 6.85e+02 dihedral pdb=" C4' U C 51 " pdb=" C3' U C 51 " pdb=" C2' U C 51 " pdb=" C1' U C 51 " ideal model delta sinusoidal sigma weight residual 36.35 -35.29 71.64 1 3.10e+00 1.04e-01 6.84e+02 dihedral pdb=" O4' U C 52 " pdb=" C4' U C 52 " pdb=" C3' U C 52 " pdb=" C2' U C 52 " ideal model delta sinusoidal sigma weight residual -35.15 23.83 -58.97 1 4.00e+00 6.25e-02 2.91e+02 ... (remaining 12461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2752 0.056 - 0.111: 422 0.111 - 0.167: 53 0.167 - 0.223: 13 0.223 - 0.278: 94 Chirality restraints: 3334 Sorted by residual: chirality pdb=" P A C 37 " pdb=" OP1 A C 37 " pdb=" OP2 A C 37 " pdb=" O5' A C 37 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C2' U C 51 " pdb=" C3' U C 51 " pdb=" O2' U C 51 " pdb=" C1' U C 51 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2' U C 52 " pdb=" C3' U C 52 " pdb=" O2' U C 52 " pdb=" C1' U C 52 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3331 not shown) Planarity restraints: 3299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1402 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A1403 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1403 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1403 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1634 " 0.015 2.00e-02 2.50e+03 1.02e-02 2.59e+00 pdb=" CG TRP A1634 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A1634 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A1634 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1634 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1634 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1634 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1634 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1634 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1634 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO A 904 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " -0.022 5.00e-02 4.00e+02 ... (remaining 3296 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 440 2.63 - 3.20: 19907 3.20 - 3.77: 35398 3.77 - 4.33: 46775 4.33 - 4.90: 70236 Nonbonded interactions: 172756 Sorted by model distance: nonbonded pdb="MG MG A1801 " pdb=" O3B ADP A1802 " model vdw 2.067 2.170 nonbonded pdb="MG MG F1801 " pdb=" O1B ADP F1802 " model vdw 2.077 2.170 nonbonded pdb=" O2' C D 27 " pdb=" OE2 GLU A 393 " model vdw 2.124 3.040 nonbonded pdb=" OG1 THR A1272 " pdb=" OG1 THR A1276 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR A 484 " pdb=" OD1 ASN A 486 " model vdw 2.160 3.040 ... (remaining 172751 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 'C' selection = (chain 'D' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name O2' or name C1' or name N9 or name C8 or \ name N7 or name C5 or name C6 or name O6 or name N1 or name C2 or name N2 or nam \ e N3 or name C4 )) or resid 2 through 52)) } 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: 1.550 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.410 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.002 0.032 20952 Z= 0.119 Angle : 0.640 12.300 28839 Z= 0.316 Chirality : 0.057 0.278 3334 Planarity : 0.004 0.043 3299 Dihedral : 14.681 93.774 8196 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.18), residues: 2221 helix: 0.60 (0.16), residues: 1046 sheet: -0.89 (0.32), residues: 250 loop : -0.83 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1448 TYR 0.013 0.001 TYR F 488 PHE 0.013 0.001 PHE F 370 TRP 0.027 0.001 TRP A1634 HIS 0.007 0.001 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (20952) covalent geometry : angle 0.63969 / 0.32 (28839) hydrogen bonds : bond 0.18998 / 10.46 ( 925) hydrogen bonds : angle 7.23556 / 4.10 ( 2557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ASP cc_start: 0.8876 (p0) cc_final: 0.8532 (p0) REVERT: A 487 MET cc_start: 0.9034 (ppp) cc_final: 0.7991 (ppp) REVERT: A 516 GLN cc_start: 0.8719 (mp10) cc_final: 0.8489 (mp10) REVERT: A 620 MET cc_start: 0.8571 (mmm) cc_final: 0.8309 (mmm) REVERT: F 138 ILE cc_start: 0.8363 (mm) cc_final: 0.8084 (tp) REVERT: F 183 ASN cc_start: 0.8823 (t0) cc_final: 0.8532 (t0) REVERT: F 208 MET cc_start: 0.8181 (mmp) cc_final: 0.7913 (mmp) REVERT: F 578 TYR cc_start: 0.8321 (t80) cc_final: 0.7860 (t80) REVERT: F 591 ILE cc_start: 0.8300 (mt) cc_final: 0.8068 (tt) REVERT: F 606 PHE cc_start: 0.8123 (m-80) cc_final: 0.7675 (m-80) outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.1349 time to fit residues: 34.6875 Evaluate side-chains 134 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 454 ASN A 520 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 GLN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 GLN ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.062392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.044520 restraints weight = 144871.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045814 restraints weight = 87573.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.046654 restraints weight = 63086.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.047196 restraints weight = 50922.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.047489 restraints weight = 44331.935| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 20952 Z= 0.286 Angle : 0.792 17.460 28839 Z= 0.378 Chirality : 0.050 0.602 3334 Planarity : 0.005 0.056 3299 Dihedral : 10.013 85.680 3691 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.39 % Favored : 93.56 % Rotamer: Outliers : 0.15 % Allowed : 6.51 % Favored : 93.34 % 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: -0.65 (0.18), residues: 2221 helix: 0.31 (0.16), residues: 1055 sheet: -1.14 (0.33), residues: 237 loop : -1.00 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1418 TYR 0.015 0.002 TYR A1000 PHE 0.019 0.002 PHE A1481 TRP 0.014 0.001 TRP A1634 HIS 0.008 0.001 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.29 (20952) covalent geometry : angle 0.79202 / 0.38 (28839) hydrogen bonds : bond 0.05438 / 3.01 ( 925) hydrogen bonds : angle 5.32957 / 2.62 ( 2557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 LYS cc_start: 0.9198 (tptp) cc_final: 0.8970 (tptp) REVERT: A 75 MET cc_start: 0.8369 (mpp) cc_final: 0.7799 (mpp) REVERT: A 208 MET cc_start: 0.8224 (tmm) cc_final: 0.7991 (ppp) REVERT: A 351 ASP cc_start: 0.9144 (p0) cc_final: 0.8791 (p0) REVERT: A 424 MET cc_start: 0.8806 (ppp) cc_final: 0.8581 (ppp) REVERT: A 487 MET cc_start: 0.8807 (ppp) cc_final: 0.8290 (ppp) REVERT: A 620 MET cc_start: 0.8792 (mmm) cc_final: 0.8479 (mmm) REVERT: A 635 MET cc_start: 0.8667 (mmm) cc_final: 0.8462 (mmm) REVERT: F 138 ILE cc_start: 0.8813 (mm) cc_final: 0.8563 (tp) REVERT: F 183 ASN cc_start: 0.8667 (t0) cc_final: 0.8220 (t0) REVERT: F 208 MET cc_start: 0.8507 (mmp) cc_final: 0.8236 (mmp) REVERT: F 227 HIS cc_start: 0.7241 (t70) cc_final: 0.6861 (t-90) REVERT: F 249 LEU cc_start: 0.9171 (tp) cc_final: 0.8929 (tp) REVERT: F 288 MET cc_start: 0.9194 (tmm) cc_final: 0.8948 (tmm) REVERT: F 360 MET cc_start: 0.9400 (mmp) cc_final: 0.9172 (mmm) REVERT: F 487 MET cc_start: 0.9214 (ppp) cc_final: 0.8949 (ppp) REVERT: F 578 TYR cc_start: 0.8488 (t80) cc_final: 0.8032 (t80) REVERT: F 591 ILE cc_start: 0.8738 (mt) cc_final: 0.8385 (tp) REVERT: F 606 PHE cc_start: 0.8195 (m-80) cc_final: 0.7841 (m-80) REVERT: F 618 ILE cc_start: 0.7846 (mp) cc_final: 0.7595 (mp) outliers start: 3 outliers final: 1 residues processed: 155 average time/residue: 0.1378 time to fit residues: 34.3585 Evaluate side-chains 128 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 67 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 102 optimal weight: 0.0030 chunk 65 optimal weight: 5.9990 chunk 61 optimal weight: 0.0060 chunk 122 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 overall best weight: 2.8012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 550 HIS A 851 ASN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 GLN ** F 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 GLN ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.063515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.045614 restraints weight = 142869.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.046978 restraints weight = 85245.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.047856 restraints weight = 60804.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.048420 restraints weight = 48735.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.048797 restraints weight = 42241.449| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20952 Z= 0.173 Angle : 0.676 11.181 28839 Z= 0.323 Chirality : 0.047 0.363 3334 Planarity : 0.004 0.045 3299 Dihedral : 9.718 76.715 3691 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % 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: -0.56 (0.18), residues: 2221 helix: 0.47 (0.16), residues: 1046 sheet: -1.28 (0.32), residues: 246 loop : -0.98 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1658 TYR 0.019 0.002 TYR F 291 PHE 0.013 0.001 PHE A 589 TRP 0.016 0.001 TRP A1634 HIS 0.006 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (20952) covalent geometry : angle 0.67565 / 0.32 (28839) hydrogen bonds : bond 0.04817 / 2.61 ( 925) hydrogen bonds : angle 4.95600 / 2.42 ( 2557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 LYS cc_start: 0.9170 (tptp) cc_final: 0.8970 (tptp) REVERT: A 208 MET cc_start: 0.8270 (tmm) cc_final: 0.7946 (ppp) REVERT: A 351 ASP cc_start: 0.9118 (p0) cc_final: 0.8844 (p0) REVERT: A 424 MET cc_start: 0.8626 (ppp) cc_final: 0.8349 (ppp) REVERT: A 487 MET cc_start: 0.8784 (ppp) cc_final: 0.8285 (ppp) REVERT: A 516 GLN cc_start: 0.9064 (mp10) cc_final: 0.8752 (mp10) REVERT: A 635 MET cc_start: 0.8671 (mmm) cc_final: 0.8413 (mmm) REVERT: F 153 PHE cc_start: 0.9101 (t80) cc_final: 0.8543 (t80) REVERT: F 154 MET cc_start: 0.9000 (mtp) cc_final: 0.8466 (ttt) REVERT: F 183 ASN cc_start: 0.8701 (t0) cc_final: 0.8182 (t0) REVERT: F 187 LYS cc_start: 0.9375 (mmtm) cc_final: 0.9137 (mmtp) REVERT: F 227 HIS cc_start: 0.7248 (t70) cc_final: 0.6929 (t-90) REVERT: F 288 MET cc_start: 0.9170 (tmm) cc_final: 0.8935 (tmm) REVERT: F 360 MET cc_start: 0.9310 (mmp) cc_final: 0.9082 (mmm) REVERT: F 487 MET cc_start: 0.9210 (ppp) cc_final: 0.8916 (ppp) REVERT: F 578 TYR cc_start: 0.8394 (t80) cc_final: 0.7958 (t80) REVERT: F 606 PHE cc_start: 0.8208 (m-80) cc_final: 0.7760 (m-80) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1443 time to fit residues: 35.7158 Evaluate side-chains 123 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 219 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 130 optimal weight: 0.2980 chunk 173 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 151 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN A 354 ASN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 HIS ** F 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 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 = 0.3547 r_free = 0.3547 target = 0.064025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.046154 restraints weight = 140385.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047461 restraints weight = 83593.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.048351 restraints weight = 59609.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.048834 restraints weight = 47765.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.049270 restraints weight = 41704.950| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20952 Z= 0.140 Angle : 0.653 10.653 28839 Z= 0.312 Chirality : 0.046 0.352 3334 Planarity : 0.004 0.065 3299 Dihedral : 9.577 70.277 3691 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % 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: -0.45 (0.18), residues: 2221 helix: 0.55 (0.16), residues: 1052 sheet: -1.24 (0.32), residues: 245 loop : -0.93 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1418 TYR 0.018 0.001 TYR A1624 PHE 0.012 0.001 PHE F 370 TRP 0.021 0.001 TRP F 97 HIS 0.006 0.001 HIS F 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (20952) covalent geometry : angle 0.65251 / 0.31 (28839) hydrogen bonds : bond 0.04309 / 2.31 ( 925) hydrogen bonds : angle 4.74299 / 2.30 ( 2557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8365 (mpp) cc_final: 0.7970 (mpp) REVERT: A 351 ASP cc_start: 0.9078 (p0) cc_final: 0.8811 (p0) REVERT: A 487 MET cc_start: 0.8701 (ppp) cc_final: 0.8387 (ppp) REVERT: A 516 GLN cc_start: 0.9052 (mp10) cc_final: 0.8714 (mp10) REVERT: A 620 MET cc_start: 0.8628 (mmm) cc_final: 0.8114 (mmm) REVERT: A 635 MET cc_start: 0.8671 (mmm) cc_final: 0.8382 (mmm) REVERT: A 849 MET cc_start: 0.8666 (mpp) cc_final: 0.8422 (mpp) REVERT: F 153 PHE cc_start: 0.9034 (t80) cc_final: 0.8428 (t80) REVERT: F 154 MET cc_start: 0.9015 (mtp) cc_final: 0.8398 (ttt) REVERT: F 183 ASN cc_start: 0.8695 (t0) cc_final: 0.8171 (t0) REVERT: F 187 LYS cc_start: 0.9338 (mmtm) cc_final: 0.9083 (mmtp) REVERT: F 208 MET cc_start: 0.8422 (mmp) cc_final: 0.8142 (mmp) REVERT: F 222 MET cc_start: 0.8504 (tmm) cc_final: 0.8221 (tmm) REVERT: F 288 MET cc_start: 0.9157 (tmm) cc_final: 0.8913 (tmm) REVERT: F 360 MET cc_start: 0.9321 (mmp) cc_final: 0.9083 (mmp) REVERT: F 393 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7694 (tm-30) REVERT: F 487 MET cc_start: 0.9185 (ppp) cc_final: 0.8886 (ppp) REVERT: F 578 TYR cc_start: 0.8424 (t80) cc_final: 0.7969 (t80) REVERT: F 606 PHE cc_start: 0.8133 (m-80) cc_final: 0.7686 (m-80) REVERT: F 635 MET cc_start: 0.6193 (tmm) cc_final: 0.5955 (tmm) outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.1444 time to fit residues: 37.3089 Evaluate side-chains 123 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 175 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 chunk 134 optimal weight: 0.0870 chunk 227 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN A 287 GLN A 354 ASN A 490 GLN A 520 GLN A 550 HIS ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 GLN ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.064501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046405 restraints weight = 139138.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047752 restraints weight = 83010.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.048657 restraints weight = 59018.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.049249 restraints weight = 47308.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.049620 restraints weight = 40863.648| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20952 Z= 0.130 Angle : 0.635 10.188 28839 Z= 0.304 Chirality : 0.045 0.351 3334 Planarity : 0.004 0.055 3299 Dihedral : 9.467 68.018 3691 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 0.10 % Allowed : 2.88 % Favored : 97.02 % 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: -0.35 (0.18), residues: 2221 helix: 0.66 (0.16), residues: 1047 sheet: -1.20 (0.32), residues: 246 loop : -0.89 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 167 TYR 0.016 0.001 TYR F 488 PHE 0.010 0.001 PHE F 502 TRP 0.021 0.001 TRP F 97 HIS 0.005 0.001 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (20952) covalent geometry : angle 0.63526 / 0.30 (28839) hydrogen bonds : bond 0.04011 / 2.14 ( 925) hydrogen bonds : angle 4.62403 / 2.22 ( 2557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8354 (mpp) cc_final: 0.7854 (mpp) REVERT: A 351 ASP cc_start: 0.9092 (p0) cc_final: 0.8803 (p0) REVERT: A 620 MET cc_start: 0.8602 (mmm) cc_final: 0.8128 (mmm) REVERT: A 635 MET cc_start: 0.8675 (mmm) cc_final: 0.8362 (mmm) REVERT: A 849 MET cc_start: 0.8637 (mpp) cc_final: 0.8394 (mpp) REVERT: A 1209 MET cc_start: 0.8618 (ppp) cc_final: 0.8376 (ppp) REVERT: F 153 PHE cc_start: 0.8967 (t80) cc_final: 0.8324 (t80) REVERT: F 154 MET cc_start: 0.9002 (mtp) cc_final: 0.8439 (ttt) REVERT: F 183 ASN cc_start: 0.8757 (t0) cc_final: 0.8189 (t0) REVERT: F 187 LYS cc_start: 0.9241 (mmtm) cc_final: 0.8970 (mmtp) REVERT: F 222 MET cc_start: 0.8534 (tmm) cc_final: 0.8189 (tmm) REVERT: F 275 SER cc_start: 0.9176 (p) cc_final: 0.8836 (p) REVERT: F 288 MET cc_start: 0.9193 (tmm) cc_final: 0.8928 (tmm) REVERT: F 360 MET cc_start: 0.9298 (mmp) cc_final: 0.8973 (mmm) REVERT: F 393 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7597 (tm-30) REVERT: F 468 ILE cc_start: 0.8646 (mp) cc_final: 0.8263 (pt) REVERT: F 487 MET cc_start: 0.9151 (ppp) cc_final: 0.8869 (ppp) REVERT: F 548 LYS cc_start: 0.9282 (ptpt) cc_final: 0.8790 (tptp) REVERT: F 578 TYR cc_start: 0.8412 (t80) cc_final: 0.7965 (t80) REVERT: F 606 PHE cc_start: 0.8115 (m-80) cc_final: 0.7673 (m-80) REVERT: F 618 ILE cc_start: 0.7611 (mt) cc_final: 0.7336 (mp) outliers start: 2 outliers final: 1 residues processed: 160 average time/residue: 0.1394 time to fit residues: 35.8885 Evaluate side-chains 128 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 46 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 155 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.063632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.045458 restraints weight = 144006.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.046797 restraints weight = 85714.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.047690 restraints weight = 61421.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.048267 restraints weight = 49486.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048582 restraints weight = 43039.237| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20952 Z= 0.193 Angle : 0.680 11.415 28839 Z= 0.327 Chirality : 0.046 0.341 3334 Planarity : 0.004 0.048 3299 Dihedral : 9.531 67.610 3691 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.12 % Favored : 93.83 % Rotamer: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.61 % 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: -0.46 (0.18), residues: 2221 helix: 0.54 (0.16), residues: 1051 sheet: -1.23 (0.32), residues: 250 loop : -0.92 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1448 TYR 0.016 0.002 TYR A1624 PHE 0.016 0.001 PHE A 589 TRP 0.021 0.001 TRP F 97 HIS 0.011 0.001 HIS F 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (20952) covalent geometry : angle 0.67966 / 0.33 (28839) hydrogen bonds : bond 0.04328 / 2.32 ( 925) hydrogen bonds : angle 4.69665 / 2.24 ( 2557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8410 (mpp) cc_final: 0.7974 (mpp) REVERT: A 351 ASP cc_start: 0.9154 (p0) cc_final: 0.8841 (p0) REVERT: A 516 GLN cc_start: 0.9076 (mp10) cc_final: 0.8775 (mp10) REVERT: A 620 MET cc_start: 0.8678 (mmm) cc_final: 0.8196 (mmm) REVERT: A 635 MET cc_start: 0.8770 (mmm) cc_final: 0.8422 (mmm) REVERT: F 63 MET cc_start: 0.6529 (mmm) cc_final: 0.5530 (mmm) REVERT: F 153 PHE cc_start: 0.9019 (t80) cc_final: 0.8386 (t80) REVERT: F 154 MET cc_start: 0.8917 (mtp) cc_final: 0.8337 (ttt) REVERT: F 183 ASN cc_start: 0.8783 (t0) cc_final: 0.8377 (t0) REVERT: F 208 MET cc_start: 0.8367 (mmp) cc_final: 0.8137 (mmp) REVERT: F 288 MET cc_start: 0.9204 (tmm) cc_final: 0.8941 (tmm) REVERT: F 360 MET cc_start: 0.9245 (mmp) cc_final: 0.9004 (mmm) REVERT: F 468 ILE cc_start: 0.8695 (mp) cc_final: 0.8343 (pt) REVERT: F 487 MET cc_start: 0.9183 (ppp) cc_final: 0.8900 (ppp) REVERT: F 548 LYS cc_start: 0.9288 (ptpt) cc_final: 0.8814 (tptp) REVERT: F 578 TYR cc_start: 0.8458 (t80) cc_final: 0.8001 (t80) REVERT: F 606 PHE cc_start: 0.8091 (m-80) cc_final: 0.7661 (m-80) REVERT: F 635 MET cc_start: 0.6249 (tmm) cc_final: 0.5902 (tmm) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1408 time to fit residues: 35.1384 Evaluate side-chains 122 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 164 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 GLN F 454 ASN ** F 471 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 = 0.3498 r_free = 0.3498 target = 0.062510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044592 restraints weight = 145247.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045890 restraints weight = 87462.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.046737 restraints weight = 62960.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.047301 restraints weight = 51006.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047615 restraints weight = 44470.453| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20952 Z= 0.253 Angle : 0.746 12.538 28839 Z= 0.361 Chirality : 0.047 0.319 3334 Planarity : 0.005 0.052 3299 Dihedral : 9.697 67.943 3691 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.29 % Rotamer: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.27 % 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: -0.73 (0.18), residues: 2221 helix: 0.31 (0.16), residues: 1055 sheet: -1.35 (0.31), residues: 258 loop : -1.06 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1448 TYR 0.018 0.002 TYR A1624 PHE 0.021 0.002 PHE A 589 TRP 0.023 0.002 TRP F 97 HIS 0.008 0.001 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.25 (20952) covalent geometry : angle 0.74555 / 0.36 (28839) hydrogen bonds : bond 0.04718 / 2.55 ( 925) hydrogen bonds : angle 4.87039 / 2.31 ( 2557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8366 (mpp) cc_final: 0.7845 (mpp) REVERT: A 351 ASP cc_start: 0.9180 (p0) cc_final: 0.8855 (p0) REVERT: A 487 MET cc_start: 0.8793 (ppp) cc_final: 0.8314 (ppp) REVERT: A 516 GLN cc_start: 0.9008 (mp10) cc_final: 0.8674 (mp10) REVERT: A 620 MET cc_start: 0.8913 (mmm) cc_final: 0.8411 (mmm) REVERT: A 635 MET cc_start: 0.8853 (mmm) cc_final: 0.8458 (mmm) REVERT: A 922 MET cc_start: 0.9060 (mpp) cc_final: 0.8679 (mpp) REVERT: A 1209 MET cc_start: 0.8564 (ppp) cc_final: 0.8173 (ppp) REVERT: F 153 PHE cc_start: 0.9067 (t80) cc_final: 0.8438 (t80) REVERT: F 154 MET cc_start: 0.8889 (mtp) cc_final: 0.8613 (mtp) REVERT: F 183 ASN cc_start: 0.8727 (t0) cc_final: 0.8307 (t0) REVERT: F 208 MET cc_start: 0.8505 (mmp) cc_final: 0.8274 (mmp) REVERT: F 222 MET cc_start: 0.8523 (tmm) cc_final: 0.8241 (tmm) REVERT: F 227 HIS cc_start: 0.7617 (t-90) cc_final: 0.7111 (t-90) REVERT: F 270 ASP cc_start: 0.8378 (p0) cc_final: 0.8175 (p0) REVERT: F 288 MET cc_start: 0.9220 (tmm) cc_final: 0.8951 (tmm) REVERT: F 360 MET cc_start: 0.9247 (mmp) cc_final: 0.9023 (mmm) REVERT: F 468 ILE cc_start: 0.8718 (mp) cc_final: 0.8380 (pt) REVERT: F 548 LYS cc_start: 0.9296 (ptpt) cc_final: 0.8833 (tppt) REVERT: F 578 TYR cc_start: 0.8528 (t80) cc_final: 0.8114 (t80) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1433 time to fit residues: 35.7922 Evaluate side-chains 129 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 113 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 GLN ** F 471 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 = 0.3528 r_free = 0.3528 target = 0.063427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.045489 restraints weight = 141115.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.046801 restraints weight = 83712.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.047719 restraints weight = 59593.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.048327 restraints weight = 47174.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.048680 restraints weight = 40714.867| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20952 Z= 0.167 Angle : 0.684 11.452 28839 Z= 0.330 Chirality : 0.046 0.303 3334 Planarity : 0.004 0.045 3299 Dihedral : 9.600 67.841 3691 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.58 % Favored : 94.37 % Rotamer: Outliers : 0.05 % Allowed : 1.39 % Favored : 98.56 % 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: -0.66 (0.18), residues: 2221 helix: 0.43 (0.16), residues: 1062 sheet: -1.36 (0.31), residues: 264 loop : -1.11 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1448 TYR 0.014 0.001 TYR A 925 PHE 0.015 0.001 PHE A 589 TRP 0.026 0.001 TRP F 97 HIS 0.004 0.001 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (20952) covalent geometry : angle 0.68378 / 0.33 (28839) hydrogen bonds : bond 0.04211 / 2.23 ( 925) hydrogen bonds : angle 4.72482 / 2.24 ( 2557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8300 (mpp) cc_final: 0.7783 (mpp) REVERT: A 351 ASP cc_start: 0.9183 (p0) cc_final: 0.8866 (p0) REVERT: A 516 GLN cc_start: 0.8927 (mp10) cc_final: 0.8596 (mp10) REVERT: A 620 MET cc_start: 0.8836 (mmm) cc_final: 0.8597 (mmm) REVERT: A 635 MET cc_start: 0.8867 (mmm) cc_final: 0.8483 (mmm) REVERT: A 922 MET cc_start: 0.9137 (mpp) cc_final: 0.8872 (mpp) REVERT: A 1389 MET cc_start: 0.9071 (mmt) cc_final: 0.8606 (mmt) REVERT: F 63 MET cc_start: 0.6475 (mmm) cc_final: 0.5599 (mmm) REVERT: F 183 ASN cc_start: 0.8664 (t0) cc_final: 0.8310 (t0) REVERT: F 208 MET cc_start: 0.8509 (mmp) cc_final: 0.8244 (mmp) REVERT: F 222 MET cc_start: 0.8506 (tmm) cc_final: 0.8156 (tmm) REVERT: F 227 HIS cc_start: 0.7485 (t-90) cc_final: 0.7040 (t70) REVERT: F 270 ASP cc_start: 0.8159 (p0) cc_final: 0.7927 (p0) REVERT: F 275 SER cc_start: 0.9195 (p) cc_final: 0.8794 (p) REVERT: F 288 MET cc_start: 0.9180 (tmm) cc_final: 0.8911 (tmm) REVERT: F 344 MET cc_start: 0.8586 (mpp) cc_final: 0.8259 (mpp) REVERT: F 360 MET cc_start: 0.9228 (mmp) cc_final: 0.8888 (mmm) REVERT: F 468 ILE cc_start: 0.8675 (mp) cc_final: 0.8322 (pt) REVERT: F 487 MET cc_start: 0.9098 (ppp) cc_final: 0.8829 (ppp) REVERT: F 548 LYS cc_start: 0.9274 (ptpt) cc_final: 0.8814 (tppt) REVERT: F 578 TYR cc_start: 0.8466 (t80) cc_final: 0.8025 (t80) REVERT: F 606 PHE cc_start: 0.7941 (m-80) cc_final: 0.7600 (m-80) REVERT: F 618 ILE cc_start: 0.7677 (mt) cc_final: 0.7324 (mt) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1414 time to fit residues: 36.3528 Evaluate side-chains 128 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 192 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 HIS A 287 GLN A 520 GLN ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 GLN ** F 471 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 = 0.3550 r_free = 0.3550 target = 0.064338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.046097 restraints weight = 140872.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.047484 restraints weight = 83182.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.048415 restraints weight = 59314.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.049019 restraints weight = 47365.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.049398 restraints weight = 40793.156| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20952 Z= 0.131 Angle : 0.659 10.046 28839 Z= 0.319 Chirality : 0.045 0.305 3334 Planarity : 0.004 0.092 3299 Dihedral : 9.480 67.551 3691 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 0.05 % Allowed : 0.60 % Favored : 99.35 % 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: -0.48 (0.18), residues: 2221 helix: 0.57 (0.16), residues: 1060 sheet: -1.23 (0.32), residues: 248 loop : -1.02 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1448 TYR 0.020 0.001 TYR F 488 PHE 0.012 0.001 PHE A 589 TRP 0.029 0.002 TRP F 97 HIS 0.012 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (20952) covalent geometry : angle 0.65942 / 0.32 (28839) hydrogen bonds : bond 0.03887 / 2.05 ( 925) hydrogen bonds : angle 4.58757 / 2.17 ( 2557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8291 (mpp) cc_final: 0.7781 (mpp) REVERT: A 351 ASP cc_start: 0.9157 (p0) cc_final: 0.8817 (p0) REVERT: A 516 GLN cc_start: 0.8992 (mp10) cc_final: 0.8641 (mp10) REVERT: A 620 MET cc_start: 0.8837 (mmm) cc_final: 0.8567 (mmm) REVERT: A 635 MET cc_start: 0.8852 (mmm) cc_final: 0.8477 (mmm) REVERT: A 744 MET cc_start: 0.8150 (ptp) cc_final: 0.7943 (ptp) REVERT: A 922 MET cc_start: 0.9128 (mpp) cc_final: 0.8875 (mpp) REVERT: A 1209 MET cc_start: 0.8389 (ppp) cc_final: 0.7924 (ppp) REVERT: A 1389 MET cc_start: 0.9018 (mmt) cc_final: 0.8546 (mmt) REVERT: F 63 MET cc_start: 0.6678 (mmm) cc_final: 0.5871 (mmm) REVERT: F 153 PHE cc_start: 0.8797 (t80) cc_final: 0.8371 (t80) REVERT: F 183 ASN cc_start: 0.8736 (t0) cc_final: 0.8313 (t0) REVERT: F 208 MET cc_start: 0.8513 (mmp) cc_final: 0.8243 (mmp) REVERT: F 227 HIS cc_start: 0.7463 (t-90) cc_final: 0.6914 (t-90) REVERT: F 270 ASP cc_start: 0.8156 (p0) cc_final: 0.7954 (p0) REVERT: F 275 SER cc_start: 0.9221 (p) cc_final: 0.8950 (t) REVERT: F 288 MET cc_start: 0.9174 (tmm) cc_final: 0.8906 (tmm) REVERT: F 344 MET cc_start: 0.8525 (mpp) cc_final: 0.8123 (mpp) REVERT: F 360 MET cc_start: 0.9216 (mmp) cc_final: 0.8882 (mmm) REVERT: F 468 ILE cc_start: 0.8654 (mp) cc_final: 0.8305 (pt) REVERT: F 487 MET cc_start: 0.9104 (ppp) cc_final: 0.8825 (ppp) REVERT: F 548 LYS cc_start: 0.9288 (ptpt) cc_final: 0.8811 (tptp) REVERT: F 578 TYR cc_start: 0.8452 (t80) cc_final: 0.8104 (t80) REVERT: F 606 PHE cc_start: 0.7936 (m-80) cc_final: 0.7559 (m-80) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1414 time to fit residues: 35.5926 Evaluate side-chains 127 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 99 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 49 optimal weight: 0.0970 chunk 112 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 124 optimal weight: 0.0980 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.063998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.045853 restraints weight = 141820.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.047192 restraints weight = 84453.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.048115 restraints weight = 60146.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048678 restraints weight = 48251.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049088 restraints weight = 41989.548| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20952 Z= 0.153 Angle : 0.668 10.619 28839 Z= 0.323 Chirality : 0.045 0.308 3334 Planarity : 0.004 0.081 3299 Dihedral : 9.470 67.925 3691 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 0.05 % Allowed : 0.30 % Favored : 99.65 % 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: -0.47 (0.18), residues: 2221 helix: 0.57 (0.16), residues: 1060 sheet: -1.23 (0.31), residues: 263 loop : -0.99 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1448 TYR 0.026 0.001 TYR F 519 PHE 0.014 0.001 PHE A 589 TRP 0.027 0.001 TRP F 97 HIS 0.005 0.001 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (20952) covalent geometry : angle 0.66818 / 0.32 (28839) hydrogen bonds : bond 0.03950 / 2.09 ( 925) hydrogen bonds : angle 4.59090 / 2.17 ( 2557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8298 (mpp) cc_final: 0.7799 (mpp) REVERT: A 351 ASP cc_start: 0.9160 (p0) cc_final: 0.8852 (p0) REVERT: A 516 GLN cc_start: 0.8972 (mp10) cc_final: 0.8611 (mp10) REVERT: A 635 MET cc_start: 0.8884 (mmm) cc_final: 0.8506 (mmm) REVERT: A 922 MET cc_start: 0.9108 (mpp) cc_final: 0.8828 (mpp) REVERT: A 1389 MET cc_start: 0.9037 (mmt) cc_final: 0.8546 (mmt) REVERT: F 63 MET cc_start: 0.6326 (mmm) cc_final: 0.5575 (mmm) REVERT: F 153 PHE cc_start: 0.8790 (t80) cc_final: 0.8346 (t80) REVERT: F 164 LYS cc_start: 0.9105 (ptpp) cc_final: 0.8766 (tptp) REVERT: F 183 ASN cc_start: 0.8721 (t0) cc_final: 0.8335 (t0) REVERT: F 208 MET cc_start: 0.8537 (mmp) cc_final: 0.8272 (mmp) REVERT: F 227 HIS cc_start: 0.7349 (t-90) cc_final: 0.7043 (t-90) REVERT: F 249 LEU cc_start: 0.9147 (tp) cc_final: 0.8923 (tp) REVERT: F 270 ASP cc_start: 0.8174 (p0) cc_final: 0.7972 (p0) REVERT: F 275 SER cc_start: 0.9204 (p) cc_final: 0.8913 (t) REVERT: F 288 MET cc_start: 0.9170 (tmm) cc_final: 0.8907 (tmm) REVERT: F 344 MET cc_start: 0.8599 (mpp) cc_final: 0.8198 (mpp) REVERT: F 360 MET cc_start: 0.9214 (mmp) cc_final: 0.8983 (mmp) REVERT: F 468 ILE cc_start: 0.8668 (mp) cc_final: 0.8313 (pt) REVERT: F 487 MET cc_start: 0.9102 (ppp) cc_final: 0.8818 (ppp) REVERT: F 548 LYS cc_start: 0.9285 (ptpt) cc_final: 0.8839 (tppt) REVERT: F 578 TYR cc_start: 0.8471 (t80) cc_final: 0.8142 (t80) REVERT: F 606 PHE cc_start: 0.7943 (m-80) cc_final: 0.7581 (m-80) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1371 time to fit residues: 34.1557 Evaluate side-chains 129 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 123 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 210 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 213 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.064435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.046479 restraints weight = 138744.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.047796 restraints weight = 83039.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048694 restraints weight = 59364.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.049286 restraints weight = 47460.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.049672 restraints weight = 40855.032| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20952 Z= 0.128 Angle : 0.649 9.829 28839 Z= 0.313 Chirality : 0.045 0.300 3334 Planarity : 0.004 0.070 3299 Dihedral : 9.410 67.683 3691 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 0.05 % Allowed : 0.30 % Favored : 99.65 % 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: -0.38 (0.18), residues: 2221 helix: 0.64 (0.16), residues: 1059 sheet: -1.22 (0.32), residues: 248 loop : -0.93 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1448 TYR 0.020 0.001 TYR F 519 PHE 0.012 0.001 PHE A 589 TRP 0.027 0.001 TRP F 97 HIS 0.005 0.001 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (20952) covalent geometry : angle 0.64938 / 0.31 (28839) hydrogen bonds : bond 0.03763 / 1.98 ( 925) hydrogen bonds : angle 4.51849 / 2.14 ( 2557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3248.43 seconds wall clock time: 57 minutes 34.98 seconds (3454.98 seconds total)