Starting phenix.real_space_refine on Sun Sep 29 00:26:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/09_2024/7w0d_32239.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/09_2024/7w0d_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/09_2024/7w0d_32239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/09_2024/7w0d_32239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/09_2024/7w0d_32239.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0d_32239/09_2024/7w0d_32239.cif" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'RNA': 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: {'RNA': 52} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 25, 'rna3p_pyr': 25} Link IDs: {'rna2p': 1, 'rna3p': 50} 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: 11.51, per 1000 atoms: 0.57 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: 5.40 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 7.95 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: 10.86 Time building geometry restraints manager: 6.24 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: 28567 2.46 - 4.92: 237 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: 11430 18.75 - 37.51: 1017 37.51 - 56.26: 201 56.26 - 75.02: 173 75.02 - 93.77: 13 Dihedral angle restraints: 12834 sinusoidal: 6257 harmonic: 6577 Sorted by residual: dihedral pdb=" CA ILE A1654 " pdb=" C ILE A1654 " pdb=" N ASN A1655 " pdb=" CA ASN A1655 " ideal model delta harmonic sigma weight residual 180.00 153.76 26.24 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" C5' ADP A1802 " pdb=" O5' ADP A1802 " pdb=" PA ADP A1802 " pdb=" O2A ADP A1802 " ideal model delta sinusoidal sigma weight residual -60.00 -153.77 93.77 1 2.00e+01 2.50e-03 2.56e+01 dihedral pdb=" CA MET A 101 " pdb=" C MET A 101 " pdb=" N TRP A 102 " pdb=" CA TRP A 102 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 12831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2253 0.032 - 0.064: 732 0.064 - 0.096: 231 0.096 - 0.128: 103 0.128 - 0.160: 15 Chirality restraints: 3334 Sorted by residual: chirality pdb=" CG LEU F 249 " pdb=" CB LEU F 249 " pdb=" CD1 LEU F 249 " pdb=" CD2 LEU F 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA MET A 208 " pdb=" N MET A 208 " pdb=" C MET A 208 " pdb=" CB MET A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ILE F 138 " pdb=" N ILE F 138 " pdb=" C ILE F 138 " pdb=" CB ILE F 138 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 55.580 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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= 0.147 Angle : 0.584 12.300 28839 Z= 0.305 Chirality : 0.039 0.160 3334 Planarity : 0.004 0.043 3299 Dihedral : 16.436 93.774 8566 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.027 0.001 TRP A1634 HIS 0.007 0.001 HIS A 550 PHE 0.013 0.001 PHE F 370 TYR 0.013 0.001 TYR F 488 ARG 0.004 0.000 ARG A1448 *********************** 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 fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 2.102 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: 0.8362 (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: 0.8122 (m-80) cc_final: 0.7675 (m-80) outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.3135 time to fit residues: 79.0207 Evaluate side-chains 134 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 chunk 181 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 210 optimal weight: 20.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20952 Z= 0.311 Angle : 0.661 11.113 28839 Z= 0.339 Chirality : 0.042 0.166 3334 Planarity : 0.005 0.048 3299 Dihedral : 15.077 83.565 4061 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.12 % Favored : 93.83 % Rotamer: Outliers : 0.10 % Allowed : 6.07 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2221 helix: 0.42 (0.16), residues: 1053 sheet: -1.07 (0.32), residues: 251 loop : -0.93 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 97 HIS 0.007 0.001 HIS A1522 PHE 0.016 0.002 PHE A 589 TYR 0.014 0.002 TYR A1000 ARG 0.006 0.001 ARG F 427 *********************** 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 158 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 LYS cc_start: 0.9134 (tptp) cc_final: 0.8884 (tptp) REVERT: A 75 MET cc_start: 0.8313 (mpp) cc_final: 0.7792 (mpp) REVERT: A 208 MET cc_start: 0.8169 (tmm) cc_final: 0.7926 (ppp) REVERT: A 351 ASP cc_start: 0.9121 (p0) cc_final: 0.8785 (p0) REVERT: A 487 MET cc_start: 0.8707 (ppp) cc_final: 0.8011 (ppp) REVERT: A 620 MET cc_start: 0.8759 (mmm) cc_final: 0.8504 (mmm) REVERT: A 635 MET cc_start: 0.8598 (mmm) cc_final: 0.8346 (mmm) REVERT: F 138 ILE cc_start: 0.8792 (mm) cc_final: 0.8492 (tp) REVERT: F 154 MET cc_start: 0.8940 (mtp) cc_final: 0.8458 (ttt) REVERT: F 183 ASN cc_start: 0.8594 (t0) cc_final: 0.8154 (t0) REVERT: F 208 MET cc_start: 0.8391 (mmp) cc_final: 0.8141 (mmp) REVERT: F 227 HIS cc_start: 0.7083 (t70) cc_final: 0.6649 (t-90) REVERT: F 243 GLU cc_start: 0.9329 (pt0) cc_final: 0.8912 (tm-30) REVERT: F 249 LEU cc_start: 0.9121 (tp) cc_final: 0.8881 (tp) REVERT: F 288 MET cc_start: 0.9041 (tmm) cc_final: 0.8806 (tmm) REVERT: F 487 MET cc_start: 0.9287 (ppp) cc_final: 0.9020 (ppp) REVERT: F 578 TYR cc_start: 0.8457 (t80) cc_final: 0.7992 (t80) REVERT: F 606 PHE cc_start: 0.8140 (m-80) cc_final: 0.7823 (m-80) outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.3109 time to fit residues: 77.9069 Evaluate side-chains 128 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 550 HIS ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20952 Z= 0.254 Angle : 0.617 11.291 28839 Z= 0.315 Chirality : 0.041 0.152 3334 Planarity : 0.004 0.061 3299 Dihedral : 14.998 76.105 4061 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.42 % Rotamer: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2221 helix: 0.47 (0.16), residues: 1046 sheet: -1.27 (0.32), residues: 246 loop : -0.94 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 97 HIS 0.006 0.001 HIS F 227 PHE 0.014 0.001 PHE A 589 TYR 0.019 0.002 TYR A 88 ARG 0.007 0.000 ARG A1658 *********************** 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 154 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 LYS cc_start: 0.9098 (tptp) cc_final: 0.8880 (tptp) REVERT: A 208 MET cc_start: 0.8240 (tmm) cc_final: 0.7923 (ppp) REVERT: A 351 ASP cc_start: 0.9114 (p0) cc_final: 0.8839 (p0) REVERT: A 487 MET cc_start: 0.8645 (ppp) cc_final: 0.8007 (ppp) REVERT: A 516 GLN cc_start: 0.8884 (mp10) cc_final: 0.8641 (mp10) REVERT: A 635 MET cc_start: 0.8618 (mmm) cc_final: 0.8380 (mmm) REVERT: F 138 ILE cc_start: 0.8708 (mm) cc_final: 0.8483 (tp) REVERT: F 153 PHE cc_start: 0.9070 (t80) cc_final: 0.8507 (t80) REVERT: F 154 MET cc_start: 0.9010 (mtp) cc_final: 0.8468 (ttt) REVERT: F 183 ASN cc_start: 0.8671 (t0) cc_final: 0.8177 (t0) REVERT: F 187 LYS cc_start: 0.9413 (mmtm) cc_final: 0.9154 (mmtp) REVERT: F 288 MET cc_start: 0.8996 (tmm) cc_final: 0.8778 (tmm) REVERT: F 360 MET cc_start: 0.9290 (mmp) cc_final: 0.9070 (mmm) REVERT: F 487 MET cc_start: 0.9276 (ppp) cc_final: 0.8978 (ppp) REVERT: F 578 TYR cc_start: 0.8396 (t80) cc_final: 0.7956 (t80) REVERT: F 591 ILE cc_start: 0.8584 (mt) cc_final: 0.8332 (tp) REVERT: F 593 TRP cc_start: 0.8871 (t-100) cc_final: 0.8655 (t-100) REVERT: F 606 PHE cc_start: 0.8150 (m-80) cc_final: 0.7756 (m-80) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.3352 time to fit residues: 80.5194 Evaluate side-chains 127 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 287 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20952 Z= 0.299 Angle : 0.645 12.013 28839 Z= 0.331 Chirality : 0.041 0.147 3334 Planarity : 0.005 0.084 3299 Dihedral : 14.971 74.672 4061 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2221 helix: 0.35 (0.16), residues: 1051 sheet: -1.29 (0.32), residues: 237 loop : -1.04 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 97 HIS 0.006 0.001 HIS A1522 PHE 0.016 0.001 PHE A 589 TYR 0.015 0.002 TYR A1000 ARG 0.006 0.001 ARG A1418 *********************** 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 148 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8321 (mpp) cc_final: 0.7948 (mpp) REVERT: A 351 ASP cc_start: 0.9142 (p0) cc_final: 0.8850 (p0) REVERT: A 487 MET cc_start: 0.8606 (ppp) cc_final: 0.8206 (ppp) REVERT: A 516 GLN cc_start: 0.8896 (mp10) cc_final: 0.8634 (mp10) REVERT: A 620 MET cc_start: 0.8667 (mmm) cc_final: 0.8258 (mmm) REVERT: A 635 MET cc_start: 0.8679 (mmm) cc_final: 0.8400 (mmm) REVERT: F 138 ILE cc_start: 0.8817 (mm) cc_final: 0.8276 (tt) REVERT: F 153 PHE cc_start: 0.9084 (t80) cc_final: 0.8523 (t80) REVERT: F 154 MET cc_start: 0.8957 (mtp) cc_final: 0.8673 (mtp) REVERT: F 183 ASN cc_start: 0.8581 (t0) cc_final: 0.8086 (t0) REVERT: F 187 LYS cc_start: 0.9395 (mmtm) cc_final: 0.9130 (mmtp) REVERT: F 208 MET cc_start: 0.8385 (mmp) cc_final: 0.8122 (mmp) REVERT: F 222 MET cc_start: 0.8523 (tmm) cc_final: 0.8207 (tmm) REVERT: F 227 HIS cc_start: 0.6908 (t-170) cc_final: 0.6697 (t-90) REVERT: F 288 MET cc_start: 0.9009 (tmm) cc_final: 0.8759 (tmm) REVERT: F 360 MET cc_start: 0.9265 (mmp) cc_final: 0.9055 (mmm) REVERT: F 487 MET cc_start: 0.9229 (ppp) cc_final: 0.8954 (ppp) REVERT: F 578 TYR cc_start: 0.8472 (t80) cc_final: 0.8031 (t80) REVERT: F 606 PHE cc_start: 0.8085 (m-80) cc_final: 0.7713 (m-80) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.3217 time to fit residues: 75.1628 Evaluate side-chains 124 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN 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** ** A1338 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 ASN ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 20952 Z= 0.436 Angle : 0.761 13.754 28839 Z= 0.390 Chirality : 0.045 0.225 3334 Planarity : 0.005 0.069 3299 Dihedral : 15.119 75.917 4061 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.29 % Favored : 92.66 % Rotamer: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2221 helix: -0.08 (0.16), residues: 1067 sheet: -1.57 (0.32), residues: 248 loop : -1.29 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 97 HIS 0.010 0.002 HIS A1522 PHE 0.025 0.002 PHE A 589 TYR 0.019 0.002 TYR A1000 ARG 0.008 0.001 ARG A 167 *********************** 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 144 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8365 (mpp) cc_final: 0.7955 (mpp) REVERT: A 208 MET cc_start: 0.8251 (tmm) cc_final: 0.7967 (tmm) REVERT: A 287 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8788 (mm-40) REVERT: A 351 ASP cc_start: 0.9091 (p0) cc_final: 0.8766 (p0) REVERT: A 458 MET cc_start: 0.9298 (tpp) cc_final: 0.9086 (tpp) REVERT: A 516 GLN cc_start: 0.8892 (mp10) cc_final: 0.8636 (mp10) REVERT: A 620 MET cc_start: 0.8751 (mmm) cc_final: 0.8386 (mmm) REVERT: A 635 MET cc_start: 0.8776 (mmm) cc_final: 0.8415 (mmm) REVERT: F 153 PHE cc_start: 0.9101 (t80) cc_final: 0.8518 (t80) REVERT: F 154 MET cc_start: 0.8924 (mtp) cc_final: 0.8656 (mtp) REVERT: F 183 ASN cc_start: 0.8605 (t0) cc_final: 0.8225 (t0) REVERT: F 288 MET cc_start: 0.9090 (tmm) cc_final: 0.8816 (tmm) REVERT: F 360 MET cc_start: 0.9209 (mmp) cc_final: 0.8991 (mmm) REVERT: F 468 ILE cc_start: 0.8730 (mp) cc_final: 0.8380 (pt) REVERT: F 578 TYR cc_start: 0.8501 (t80) cc_final: 0.8067 (t80) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.3327 time to fit residues: 76.7999 Evaluate side-chains 121 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2197 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= 0.228 Angle : 0.627 11.872 28839 Z= 0.322 Chirality : 0.041 0.190 3334 Planarity : 0.004 0.039 3299 Dihedral : 15.134 76.407 4061 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2221 helix: 0.28 (0.16), residues: 1061 sheet: -1.42 (0.31), residues: 248 loop : -1.15 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 97 HIS 0.004 0.001 HIS A 576 PHE 0.014 0.001 PHE A 589 TYR 0.013 0.001 TYR A1000 ARG 0.004 0.000 ARG A1448 *********************** 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 157 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8305 (mpp) cc_final: 0.7904 (mpp) REVERT: A 351 ASP cc_start: 0.9139 (p0) cc_final: 0.8836 (p0) REVERT: A 487 MET cc_start: 0.8800 (ppp) cc_final: 0.8113 (ppp) REVERT: A 620 MET cc_start: 0.8772 (mmm) cc_final: 0.8557 (mmm) REVERT: A 635 MET cc_start: 0.8770 (mmm) cc_final: 0.8477 (mmm) REVERT: F 138 ILE cc_start: 0.8607 (mm) cc_final: 0.8312 (tp) REVERT: F 153 PHE cc_start: 0.9090 (t80) cc_final: 0.8480 (t80) REVERT: F 154 MET cc_start: 0.8961 (mtp) cc_final: 0.8686 (mtp) REVERT: F 183 ASN cc_start: 0.8730 (t0) cc_final: 0.8325 (t0) REVERT: F 222 MET cc_start: 0.8514 (tmm) cc_final: 0.8188 (tmm) REVERT: F 288 MET cc_start: 0.9050 (tmm) cc_final: 0.8778 (tmm) REVERT: F 360 MET cc_start: 0.9188 (mmp) cc_final: 0.8842 (mmm) REVERT: F 468 ILE cc_start: 0.8693 (mp) cc_final: 0.8339 (pt) REVERT: F 487 MET cc_start: 0.9163 (ppp) cc_final: 0.8883 (ppp) REVERT: F 578 TYR cc_start: 0.8410 (t80) cc_final: 0.7969 (t80) REVERT: F 591 ILE cc_start: 0.8694 (mt) cc_final: 0.8374 (tp) REVERT: F 606 PHE cc_start: 0.7879 (m-80) cc_final: 0.7558 (m-80) REVERT: F 635 MET cc_start: 0.6448 (tmm) cc_final: 0.6189 (tmm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3243 time to fit residues: 80.5568 Evaluate side-chains 124 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 223 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 136 optimal weight: 0.0770 chunk 103 optimal weight: 7.9990 chunk 138 optimal weight: 0.7980 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 GLN ** A 934 HIS ** 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 313 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2227 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= 0.169 Angle : 0.602 10.482 28839 Z= 0.307 Chirality : 0.040 0.184 3334 Planarity : 0.004 0.044 3299 Dihedral : 14.995 74.504 4061 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 0.05 % Allowed : 1.34 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2221 helix: 0.53 (0.16), residues: 1048 sheet: -1.31 (0.31), residues: 247 loop : -0.99 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 97 HIS 0.007 0.001 HIS A 550 PHE 0.013 0.001 PHE A 551 TYR 0.014 0.001 TYR F 488 ARG 0.004 0.000 ARG A1448 *********************** 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 158 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8245 (mpp) cc_final: 0.7728 (mpp) REVERT: A 208 MET cc_start: 0.8116 (tmm) cc_final: 0.7915 (tmm) REVERT: A 351 ASP cc_start: 0.9125 (p0) cc_final: 0.8839 (p0) REVERT: A 516 GLN cc_start: 0.8947 (mp10) cc_final: 0.8678 (mp10) REVERT: A 620 MET cc_start: 0.8740 (mmm) cc_final: 0.8487 (mmm) REVERT: A 635 MET cc_start: 0.8746 (mmm) cc_final: 0.8473 (mmm) REVERT: A 1389 MET cc_start: 0.8849 (mmt) cc_final: 0.8459 (mmt) REVERT: F 153 PHE cc_start: 0.9002 (t80) cc_final: 0.8363 (t80) REVERT: F 154 MET cc_start: 0.8965 (mtp) cc_final: 0.8711 (mtp) REVERT: F 183 ASN cc_start: 0.8702 (t0) cc_final: 0.8278 (t0) REVERT: F 288 MET cc_start: 0.9020 (tmm) cc_final: 0.8759 (tmm) REVERT: F 344 MET cc_start: 0.8521 (mpp) cc_final: 0.8156 (mpp) REVERT: F 360 MET cc_start: 0.9161 (mmp) cc_final: 0.8823 (mmm) REVERT: F 468 ILE cc_start: 0.8613 (mp) cc_final: 0.8259 (pt) REVERT: F 487 MET cc_start: 0.9208 (ppp) cc_final: 0.8919 (ppp) REVERT: F 578 TYR cc_start: 0.8380 (t80) cc_final: 0.7921 (t80) REVERT: F 606 PHE cc_start: 0.7922 (m-80) cc_final: 0.7601 (m-80) REVERT: F 635 MET cc_start: 0.6420 (tmm) cc_final: 0.6089 (tmm) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.3148 time to fit residues: 78.8009 Evaluate side-chains 126 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 110 optimal weight: 0.0670 chunk 20 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 934 HIS ** 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20952 Z= 0.215 Angle : 0.608 11.111 28839 Z= 0.313 Chirality : 0.041 0.165 3334 Planarity : 0.004 0.095 3299 Dihedral : 14.919 74.292 4061 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.94 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2221 helix: 0.54 (0.16), residues: 1049 sheet: -1.34 (0.31), residues: 254 loop : -0.95 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 97 HIS 0.009 0.001 HIS F 227 PHE 0.014 0.001 PHE A 589 TYR 0.017 0.001 TYR A 925 ARG 0.007 0.000 ARG A1448 *********************** 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 153 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8283 (mpp) cc_final: 0.7792 (mpp) REVERT: A 208 MET cc_start: 0.8107 (tmm) cc_final: 0.7894 (tmm) REVERT: A 351 ASP cc_start: 0.9123 (p0) cc_final: 0.8817 (p0) REVERT: A 516 GLN cc_start: 0.8821 (mp10) cc_final: 0.8525 (mp10) REVERT: A 635 MET cc_start: 0.8821 (mmm) cc_final: 0.8473 (mmm) REVERT: F 153 PHE cc_start: 0.9003 (t80) cc_final: 0.8380 (t80) REVERT: F 154 MET cc_start: 0.8924 (mtp) cc_final: 0.8658 (mtp) REVERT: F 183 ASN cc_start: 0.8565 (t0) cc_final: 0.8237 (t0) REVERT: F 222 MET cc_start: 0.9045 (tmm) cc_final: 0.8843 (tmm) REVERT: F 275 SER cc_start: 0.9228 (p) cc_final: 0.8931 (p) REVERT: F 288 MET cc_start: 0.9032 (tmm) cc_final: 0.8763 (tmm) REVERT: F 360 MET cc_start: 0.9158 (mmp) cc_final: 0.8829 (mmm) REVERT: F 468 ILE cc_start: 0.8690 (mp) cc_final: 0.8339 (pt) REVERT: F 487 MET cc_start: 0.9172 (ppp) cc_final: 0.8899 (ppp) REVERT: F 578 TYR cc_start: 0.8364 (t80) cc_final: 0.7929 (t80) REVERT: F 606 PHE cc_start: 0.7936 (m-80) cc_final: 0.7614 (m-80) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3119 time to fit residues: 76.0797 Evaluate side-chains 125 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.0670 chunk 208 optimal weight: 0.4980 chunk 214 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 GLN A 734 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20952 Z= 0.158 Angle : 0.599 9.221 28839 Z= 0.306 Chirality : 0.040 0.173 3334 Planarity : 0.004 0.071 3299 Dihedral : 14.871 74.281 4061 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2221 helix: 0.60 (0.16), residues: 1061 sheet: -1.26 (0.31), residues: 254 loop : -0.89 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 97 HIS 0.005 0.001 HIS A 550 PHE 0.010 0.001 PHE F 153 TYR 0.019 0.001 TYR F 488 ARG 0.004 0.000 ARG A1448 *********************** 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 155 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.203 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: 0.8276 (mpp) cc_final: 0.7781 (mpp) REVERT: A 351 ASP cc_start: 0.9103 (p0) cc_final: 0.8820 (p0) REVERT: A 516 GLN cc_start: 0.8865 (mp10) cc_final: 0.8595 (mp10) REVERT: A 635 MET cc_start: 0.8754 (mmm) cc_final: 0.8422 (mmm) REVERT: A 1209 MET cc_start: 0.8288 (ppp) cc_final: 0.7852 (ppp) REVERT: F 63 MET cc_start: 0.6164 (mmm) cc_final: 0.5274 (mmm) REVERT: F 183 ASN cc_start: 0.8640 (t0) cc_final: 0.8250 (t0) REVERT: F 222 MET cc_start: 0.9039 (tmm) cc_final: 0.8835 (tmm) REVERT: F 227 HIS cc_start: 0.7252 (t-90) cc_final: 0.6791 (t-90) REVERT: F 249 LEU cc_start: 0.9073 (tp) cc_final: 0.8838 (tp) REVERT: F 275 SER cc_start: 0.9217 (p) cc_final: 0.8927 (p) REVERT: F 288 MET cc_start: 0.8949 (tmm) cc_final: 0.8677 (tmm) REVERT: F 337 LEU cc_start: 0.8686 (pp) cc_final: 0.7861 (tt) REVERT: F 344 MET cc_start: 0.8509 (mpp) cc_final: 0.8277 (mpp) REVERT: F 360 MET cc_start: 0.9139 (mmp) cc_final: 0.8818 (mmp) REVERT: F 468 ILE cc_start: 0.8538 (mp) cc_final: 0.8194 (pt) REVERT: F 487 MET cc_start: 0.9195 (ppp) cc_final: 0.8925 (ppp) REVERT: F 578 TYR cc_start: 0.8333 (t80) cc_final: 0.7889 (t80) REVERT: F 606 PHE cc_start: 0.7948 (m-80) cc_final: 0.7618 (m-80) REVERT: F 635 MET cc_start: 0.6432 (tmm) cc_final: 0.6087 (tmm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.3155 time to fit residues: 77.9163 Evaluate side-chains 125 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 231 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A 520 GLN ** A 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2540 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= 0.330 Angle : 0.684 12.245 28839 Z= 0.354 Chirality : 0.042 0.160 3334 Planarity : 0.005 0.082 3299 Dihedral : 14.883 74.830 4061 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.84 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2221 helix: 0.35 (0.16), residues: 1063 sheet: -1.36 (0.31), residues: 251 loop : -1.01 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 97 HIS 0.008 0.001 HIS A1522 PHE 0.021 0.002 PHE A 589 TYR 0.023 0.002 TYR F 519 ARG 0.008 0.001 ARG A1448 ********************** 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 152 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8327 (mpp) cc_final: 0.7916 (mpp) REVERT: A 351 ASP cc_start: 0.9171 (p0) cc_final: 0.8819 (p0) REVERT: A 516 GLN cc_start: 0.8847 (mp10) cc_final: 0.8538 (mp10) REVERT: A 620 MET cc_start: 0.8921 (mmm) cc_final: 0.8627 (mmm) REVERT: A 635 MET cc_start: 0.8844 (mmm) cc_final: 0.8467 (mmm) REVERT: A 1389 MET cc_start: 0.9137 (mmt) cc_final: 0.8842 (mmt) REVERT: F 63 MET cc_start: 0.6481 (mmm) cc_final: 0.5544 (mmm) REVERT: F 164 LYS cc_start: 0.8970 (ptpp) cc_final: 0.8657 (tptp) REVERT: F 183 ASN cc_start: 0.8640 (t0) cc_final: 0.8256 (t0) REVERT: F 227 HIS cc_start: 0.7191 (t-90) cc_final: 0.6689 (t-90) REVERT: F 275 SER cc_start: 0.9231 (p) cc_final: 0.8871 (p) REVERT: F 288 MET cc_start: 0.9044 (tmm) cc_final: 0.8764 (tmm) REVERT: F 344 MET cc_start: 0.8689 (mpp) cc_final: 0.8297 (mpp) REVERT: F 360 MET cc_start: 0.9188 (mmp) cc_final: 0.8954 (mmp) REVERT: F 468 ILE cc_start: 0.8676 (mp) cc_final: 0.8331 (pt) REVERT: F 487 MET cc_start: 0.9182 (ppp) cc_final: 0.8891 (ppp) REVERT: F 578 TYR cc_start: 0.8452 (t80) cc_final: 0.8052 (t80) REVERT: F 606 PHE cc_start: 0.7996 (m-80) cc_final: 0.7673 (m-80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.3163 time to fit residues: 76.3852 Evaluate side-chains 125 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 169 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 161 optimal weight: 0.0060 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN ** A 934 HIS ** 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 = 0.3548 r_free = 0.3548 target = 0.064290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.046119 restraints weight = 142204.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.047479 restraints weight = 83972.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.048403 restraints weight = 60043.499| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20952 Z= 0.190 Angle : 0.621 10.858 28839 Z= 0.318 Chirality : 0.041 0.164 3334 Planarity : 0.004 0.070 3299 Dihedral : 14.939 75.825 4061 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2221 helix: 0.48 (0.16), residues: 1061 sheet: -1.27 (0.31), residues: 254 loop : -0.97 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 97 HIS 0.005 0.001 HIS A 143 PHE 0.013 0.001 PHE A 589 TYR 0.022 0.001 TYR F 519 ARG 0.006 0.000 ARG A1448 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3146.25 seconds wall clock time: 60 minutes 36.52 seconds (3636.52 seconds total)