Starting phenix.real_space_refine on Thu Sep 26 23:36:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0f_32241/09_2024/7w0f_32241.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0f_32241/09_2024/7w0f_32241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0f_32241/09_2024/7w0f_32241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0f_32241/09_2024/7w0f_32241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0f_32241/09_2024/7w0f_32241.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0f_32241/09_2024/7w0f_32241.cif" } resolution = 4.55 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= 0.001 sd= 0.034 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: 5 Type Number sf(0) Gaussians P 93 5.49 5 S 63 5.16 5 C 8659 2.51 5 N 2406 2.21 5 O 2876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14097 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1476, 11963 Classifications: {'peptide': 1476} Link IDs: {'PTRANS': 61, 'TRANS': 1414} Chain breaks: 2 Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 451 Classifications: {'RNA': 21} Modifications used: {'5*END': 1, 'rna3p_pur': 13, 'rna3p_pyr': 8} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 437 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 14} Link IDs: {'rna3p': 20} Chain: "E" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 544 Classifications: {'RNA': 26} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 16} Link IDs: {'rna3p': 25} Chain: "F" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 559 Classifications: {'RNA': 26} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna3p': 25} Time building chain proxies: 8.61, per 1000 atoms: 0.61 Number of scatterers: 14097 At special positions: 0 Unit cell: (92.88, 97.2, 179.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 93 15.00 O 2876 8.00 N 2406 7.00 C 8659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.3 seconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 9 sheets defined 54.8% alpha, 9.7% beta 27 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 5.78 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.785A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 80 removed outlier: 4.065A pdb=" N CYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 115 through 125 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: 3.745A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.508A pdb=" N LYS A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 4.661A pdb=" N ASN A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 232 through 251 removed outlier: 4.059A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 removed outlier: 5.243A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 313 removed outlier: 3.746A pdb=" N ILE A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 344 removed outlier: 3.799A pdb=" N LYS A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 394 through 411 removed outlier: 3.602A pdb=" N ASN A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 removed outlier: 4.575A pdb=" N ASN A 417 " --> pdb=" O PRO A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 510 through 529 removed outlier: 4.372A pdb=" N ALA A 529 " --> pdb=" O HIS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 535 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.997A pdb=" N ILE A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 553 " --> pdb=" O GLY A 549 " (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 580 removed outlier: 3.553A pdb=" N ILE A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 removed outlier: 3.699A pdb=" N ARG A 602 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 668 through 681 removed outlier: 3.672A pdb=" N VAL A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 removed outlier: 3.786A pdb=" N LYS A 685 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 741 through 750 removed outlier: 4.167A pdb=" N LEU A 748 " --> pdb=" O MET A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 Processing helix chain 'A' and resid 845 through 852 removed outlier: 3.699A pdb=" N MET A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 873 through 877 removed outlier: 3.525A pdb=" N PHE A 877 " --> pdb=" O PRO A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 926 Processing helix chain 'A' and resid 927 through 929 No H-bonds generated for 'chain 'A' and resid 927 through 929' Processing helix chain 'A' and resid 954 through 958 removed outlier: 3.995A pdb=" N GLY A 957 " --> pdb=" O HIS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 974 No H-bonds generated for 'chain 'A' and resid 972 through 974' Processing helix chain 'A' and resid 983 through 990 removed outlier: 3.807A pdb=" N LYS A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1015 removed outlier: 4.132A pdb=" N ARG A 998 " --> pdb=" O SER A 994 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1001 " --> pdb=" O ASN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1024 Processing helix chain 'A' and resid 1034 through 1038 removed outlier: 3.622A pdb=" N SER A1038 " --> pdb=" O ILE A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1179 removed outlier: 4.158A pdb=" N LYS A1179 " --> pdb=" O LEU A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1200 through 1204 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.690A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1249 removed outlier: 4.210A pdb=" N LYS A1246 " --> pdb=" O GLU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1260 Processing helix chain 'A' and resid 1261 through 1266 removed outlier: 4.179A pdb=" N LYS A1264 " --> pdb=" O ASP A1261 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A1266 " --> pdb=" O PRO A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1294 Processing helix chain 'A' and resid 1295 through 1299 Processing helix chain 'A' and resid 1303 through 1308 Processing helix chain 'A' and resid 1313 through 1319 removed outlier: 3.588A pdb=" N VAL A1319 " --> pdb=" O GLU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1339 removed outlier: 4.609A pdb=" N CYS A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG A1336 " --> pdb=" O VAL A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1356 removed outlier: 3.646A pdb=" N VAL A1356 " --> pdb=" O ASN A1353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1353 through 1356' Processing helix chain 'A' and resid 1363 through 1393 removed outlier: 7.262A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A1392 " --> pdb=" O LYS A1388 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A1393 " --> pdb=" O MET A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.580A pdb=" N ILE A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP A1427 " --> pdb=" O THR A1423 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1441 removed outlier: 4.343A pdb=" N ASN A1439 " --> pdb=" O TYR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1454 Processing helix chain 'A' and resid 1461 through 1466 Processing helix chain 'A' and resid 1468 through 1490 removed outlier: 3.583A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1508 Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1520 through 1524 removed outlier: 3.873A pdb=" N PHE A1523 " --> pdb=" O ARG A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1546 removed outlier: 3.929A pdb=" N GLU A1534 " --> pdb=" O ALA A1530 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A1536 " --> pdb=" O LEU A1532 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A1537 " --> pdb=" O SER A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1606 removed outlier: 3.990A pdb=" N ASN A1605 " --> pdb=" O MET A1602 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A1606 " --> pdb=" O SER A1603 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1602 through 1606' Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 4.210A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS A1627 " --> pdb=" O VAL A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1648 removed outlier: 3.762A pdb=" N THR A1633 " --> pdb=" O ASP A1629 " (cutoff:3.500A) Proline residue: A1643 - end of helix removed outlier: 3.599A pdb=" N GLN A1646 " --> pdb=" O GLU A1642 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 3.504A pdb=" N GLY A 114 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG A 59 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A 136 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 61 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE A 138 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N MET A 63 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 24 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 172 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE A 25 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 424 removed outlier: 5.986A pdb=" N GLN A 422 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ALA A 507 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 357 " --> pdb=" O MET A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.529A pdb=" N PHE A 558 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA6, first strand: chain 'A' and resid 768 through 771 Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.772A pdb=" N ILE A 729 " --> pdb=" O TYR A 754 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN A 753 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 830 " --> pdb=" O LEU A 757 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AA9, first strand: chain 'A' and resid 969 through 971 removed outlier: 4.512A pdb=" N VAL A 969 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET A 939 " --> pdb=" O HIS A 899 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 895 " --> pdb=" O LYS A 880 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LYS A 880 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 8.09 Time building geometry restraints manager: 4.16 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: 3075 1.33 - 1.45: 3639 1.45 - 1.57: 7591 1.57 - 1.70: 183 1.70 - 1.82: 99 Bond restraints: 14587 Sorted by residual: bond pdb=" CA PHE A 663 " pdb=" C PHE A 663 " ideal model delta sigma weight residual 1.531 1.494 0.037 1.08e-02 8.57e+03 1.18e+01 bond pdb=" N LYS A1531 " pdb=" CA LYS A1531 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 9.03e+00 bond pdb=" N ASN A1495 " pdb=" CA ASN A1495 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.14e-02 7.69e+03 7.18e+00 bond pdb=" N LEU A1499 " pdb=" CA LEU A1499 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.71e+00 bond pdb=" CA VAL A 678 " pdb=" C VAL A 678 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.27e-02 6.20e+03 5.31e+00 ... (remaining 14582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 20075 3.31 - 6.61: 90 6.61 - 9.92: 11 9.92 - 13.23: 2 13.23 - 16.53: 2 Bond angle restraints: 20180 Sorted by residual: angle pdb=" C LYS A1531 " pdb=" CA LYS A1531 " pdb=" CB LYS A1531 " ideal model delta sigma weight residual 110.85 94.32 16.53 1.70e+00 3.46e-01 9.46e+01 angle pdb=" N GLY A 657 " pdb=" CA GLY A 657 " pdb=" C GLY A 657 " ideal model delta sigma weight residual 114.92 103.84 11.08 1.30e+00 5.92e-01 7.27e+01 angle pdb=" CB LYS A1531 " pdb=" CG LYS A1531 " pdb=" CD LYS A1531 " ideal model delta sigma weight residual 111.30 126.04 -14.74 2.30e+00 1.89e-01 4.10e+01 angle pdb=" N ARG A 671 " pdb=" CA ARG A 671 " pdb=" C ARG A 671 " ideal model delta sigma weight residual 111.11 103.59 7.52 1.20e+00 6.94e-01 3.93e+01 angle pdb=" C4' C F 22 " pdb=" C3' C F 22 " pdb=" O3' C F 22 " ideal model delta sigma weight residual 113.00 104.49 8.51 1.50e+00 4.44e-01 3.22e+01 ... (remaining 20175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7841 17.89 - 35.78: 728 35.78 - 53.67: 213 53.67 - 71.56: 122 71.56 - 89.45: 42 Dihedral angle restraints: 8946 sinusoidal: 4548 harmonic: 4398 Sorted by residual: dihedral pdb=" C LYS A1531 " pdb=" N LYS A1531 " pdb=" CA LYS A1531 " pdb=" CB LYS A1531 " ideal model delta harmonic sigma weight residual -122.60 -105.44 -17.16 0 2.50e+00 1.60e-01 4.71e+01 dihedral pdb=" CA PHE A 938 " pdb=" C PHE A 938 " pdb=" N MET A 939 " pdb=" CA MET A 939 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASP A 936 " pdb=" C ASP A 936 " pdb=" N LYS A 937 " pdb=" CA LYS A 937 " ideal model delta harmonic sigma weight residual 180.00 156.07 23.93 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 8943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2113 0.066 - 0.131: 205 0.131 - 0.197: 21 0.197 - 0.262: 3 0.262 - 0.328: 2 Chirality restraints: 2344 Sorted by residual: chirality pdb=" CB ILE A 813 " pdb=" CA ILE A 813 " pdb=" CG1 ILE A 813 " pdb=" CG2 ILE A 813 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA LYS A1531 " pdb=" N LYS A1531 " pdb=" C LYS A1531 " pdb=" CB LYS A1531 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA VAL A 678 " pdb=" N VAL A 678 " pdb=" C VAL A 678 " pdb=" CB VAL A 678 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2341 not shown) Planarity restraints: 2238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 656 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C LEU A 656 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU A 656 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 657 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 591 " 0.036 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 592 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 592 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 592 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1367 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C ALA A1367 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA A1367 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A1368 " 0.009 2.00e-02 2.50e+03 ... (remaining 2235 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.06: 15 2.06 - 2.77: 2847 2.77 - 3.48: 20708 3.48 - 4.19: 35220 4.19 - 4.90: 57724 Nonbonded interactions: 116514 Sorted by model distance: nonbonded pdb=" O THR A 584 " pdb=" CD LYS A1415 " model vdw 1.356 3.440 nonbonded pdb=" NZ LYS A 966 " pdb=" O6 G C 1 " model vdw 1.361 3.120 nonbonded pdb=" OD1 ASN A1508 " pdb=" O3' U C 20 " model vdw 1.405 3.040 nonbonded pdb=" CG ASN A1508 " pdb=" O3' U C 20 " model vdw 1.495 3.270 nonbonded pdb=" OG SER A1038 " pdb=" C5' C C 11 " model vdw 1.651 3.440 ... (remaining 116509 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 40.470 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3794 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 : 0.003 0.053 14587 Z= 0.173 Angle : 0.636 16.535 20180 Z= 0.355 Chirality : 0.041 0.328 2344 Planarity : 0.004 0.056 2238 Dihedral : 17.272 89.451 6094 Min Nonbonded Distance : 1.356 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.81 % Allowed : 4.45 % Favored : 94.74 % Rotamer: Outliers : 1.19 % Allowed : 0.74 % Favored : 98.06 % Cbeta Deviations : 0.07 % 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: -0.94 (0.22), residues: 1484 helix: -0.01 (0.21), residues: 660 sheet: -0.60 (0.39), residues: 159 loop : -1.18 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1634 HIS 0.005 0.001 HIS A 18 PHE 0.017 0.001 PHE A 938 TYR 0.017 0.001 TYR A 740 ARG 0.004 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: -0.4959 (tpt) cc_final: -0.5546 (tpt) REVERT: A 675 ILE cc_start: 0.5073 (OUTLIER) cc_final: 0.4866 (mm) REVERT: A 1241 THR cc_start: 0.7890 (m) cc_final: 0.7202 (p) outliers start: 16 outliers final: 6 residues processed: 190 average time/residue: 0.3144 time to fit residues: 82.9807 Evaluate side-chains 96 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 40.0000 chunk 118 optimal weight: 30.0000 chunk 65 optimal weight: 30.0000 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 0.0770 chunk 47 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 overall best weight: 1.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 HIS A1013 ASN A1385 HIS ** A1552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3899 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14587 Z= 0.204 Angle : 0.679 18.554 20180 Z= 0.340 Chirality : 0.042 0.237 2344 Planarity : 0.005 0.078 2238 Dihedral : 16.077 81.314 3078 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Rotamer: Outliers : 0.30 % Allowed : 4.39 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.22), residues: 1484 helix: 0.06 (0.20), residues: 676 sheet: -0.55 (0.37), residues: 161 loop : -1.13 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 986 HIS 0.007 0.001 HIS A 335 PHE 0.023 0.001 PHE A1387 TYR 0.021 0.001 TYR A1232 ARG 0.016 0.001 ARG A1503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8405 (m-30) cc_final: 0.8010 (m-30) REVERT: A 186 THR cc_start: 0.6158 (p) cc_final: 0.5394 (p) REVERT: A 458 MET cc_start: -0.4664 (tpt) cc_final: -0.5132 (tpt) REVERT: A 625 MET cc_start: 0.2930 (ptt) cc_final: 0.2584 (ptt) outliers start: 4 outliers final: 0 residues processed: 119 average time/residue: 0.3272 time to fit residues: 54.8378 Evaluate side-chains 82 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 40.0000 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 153 optimal weight: 30.0000 chunk 126 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 HIS A1548 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4259 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14587 Z= 0.250 Angle : 0.702 10.553 20180 Z= 0.361 Chirality : 0.042 0.190 2344 Planarity : 0.005 0.085 2238 Dihedral : 16.401 87.923 3078 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 0.22 % Allowed : 5.51 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.22), residues: 1484 helix: -0.16 (0.19), residues: 678 sheet: -0.98 (0.38), residues: 160 loop : -0.83 (0.27), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 986 HIS 0.011 0.002 HIS A 323 PHE 0.022 0.002 PHE A1387 TYR 0.031 0.002 TYR A 521 ARG 0.008 0.001 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8419 (m-30) cc_final: 0.8119 (p0) REVERT: A 241 GLU cc_start: 0.8265 (pm20) cc_final: 0.7532 (pm20) REVERT: A 336 LEU cc_start: 0.8959 (mt) cc_final: 0.8755 (mt) REVERT: A 458 MET cc_start: -0.4495 (tpt) cc_final: -0.5289 (tpt) REVERT: A 625 MET cc_start: 0.2889 (ptt) cc_final: 0.2096 (ptt) REVERT: A 992 LEU cc_start: 0.7563 (tt) cc_final: 0.7303 (tt) outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.3049 time to fit residues: 42.2869 Evaluate side-chains 77 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 0.4980 chunk 150 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS A 490 GLN ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4276 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14587 Z= 0.201 Angle : 0.623 8.563 20180 Z= 0.321 Chirality : 0.041 0.183 2344 Planarity : 0.004 0.068 2238 Dihedral : 16.536 89.206 3078 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 0.15 % Allowed : 3.35 % Favored : 96.50 % 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: -0.73 (0.22), residues: 1484 helix: 0.14 (0.20), residues: 675 sheet: -1.06 (0.37), residues: 166 loop : -0.87 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 986 HIS 0.005 0.001 HIS A 803 PHE 0.027 0.002 PHE A1387 TYR 0.037 0.002 TYR A 521 ARG 0.006 0.001 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8356 (m-30) cc_final: 0.8112 (p0) REVERT: A 309 ILE cc_start: 0.6736 (pt) cc_final: 0.6535 (pt) REVERT: A 625 MET cc_start: 0.2760 (ptt) cc_final: 0.1985 (ptt) outliers start: 2 outliers final: 0 residues processed: 91 average time/residue: 0.2984 time to fit residues: 39.9318 Evaluate side-chains 74 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4305 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14587 Z= 0.179 Angle : 0.613 11.225 20180 Z= 0.313 Chirality : 0.040 0.217 2344 Planarity : 0.004 0.064 2238 Dihedral : 16.534 87.757 3078 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: -0.68 (0.22), residues: 1484 helix: 0.15 (0.20), residues: 676 sheet: -0.88 (0.39), residues: 153 loop : -0.87 (0.26), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 986 HIS 0.005 0.001 HIS A 323 PHE 0.020 0.001 PHE A1387 TYR 0.032 0.002 TYR A 521 ARG 0.005 0.000 ARG A1251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8274 (m-30) cc_final: 0.8030 (p0) REVERT: A 186 THR cc_start: 0.6517 (p) cc_final: 0.6152 (p) REVERT: A 241 GLU cc_start: 0.8328 (pm20) cc_final: 0.7724 (pm20) REVERT: A 244 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8774 (mttt) REVERT: A 625 MET cc_start: 0.2699 (ptt) cc_final: 0.1983 (ptt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3292 time to fit residues: 41.7099 Evaluate side-chains 76 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 88 optimal weight: 40.0000 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 0.1980 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN A 520 GLN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS A 841 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4545 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 14587 Z= 0.272 Angle : 0.694 10.112 20180 Z= 0.359 Chirality : 0.043 0.192 2344 Planarity : 0.005 0.066 2238 Dihedral : 16.782 85.309 3078 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.54 % 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: -0.87 (0.22), residues: 1484 helix: -0.00 (0.19), residues: 683 sheet: -1.21 (0.39), residues: 150 loop : -0.92 (0.27), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 986 HIS 0.014 0.002 HIS A 335 PHE 0.024 0.002 PHE A1387 TYR 0.035 0.002 TYR A1449 ARG 0.005 0.001 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.7025 (tmm) cc_final: 0.6627 (tmm) REVERT: A 238 ILE cc_start: 0.2907 (pt) cc_final: 0.2672 (pt) REVERT: A 241 GLU cc_start: 0.8338 (pm20) cc_final: 0.7792 (pm20) REVERT: A 620 MET cc_start: -0.2982 (tpp) cc_final: -0.4062 (mmt) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.3080 time to fit residues: 38.6702 Evaluate side-chains 73 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 69 optimal weight: 0.0370 chunk 93 optimal weight: 4.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4565 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14587 Z= 0.226 Angle : 0.654 8.787 20180 Z= 0.341 Chirality : 0.042 0.211 2344 Planarity : 0.004 0.064 2238 Dihedral : 16.963 84.388 3078 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer: Outliers : 0.07 % Allowed : 2.01 % Favored : 97.92 % 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: -0.93 (0.22), residues: 1484 helix: 0.03 (0.19), residues: 683 sheet: -1.58 (0.38), residues: 165 loop : -0.93 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 986 HIS 0.006 0.001 HIS A 934 PHE 0.022 0.002 PHE A1387 TYR 0.028 0.002 TYR A 521 ARG 0.004 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 MET cc_start: -0.3059 (tpp) cc_final: -0.4178 (mmt) outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.3059 time to fit residues: 37.6402 Evaluate side-chains 70 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 30.0000 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4594 moved from start: 0.6780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14587 Z= 0.219 Angle : 0.656 10.130 20180 Z= 0.343 Chirality : 0.042 0.205 2344 Planarity : 0.004 0.062 2238 Dihedral : 17.006 83.990 3078 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.53 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -0.95 (0.22), residues: 1484 helix: 0.02 (0.19), residues: 688 sheet: -1.57 (0.41), residues: 146 loop : -0.99 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 986 HIS 0.015 0.002 HIS A 800 PHE 0.030 0.002 PHE A 362 TYR 0.028 0.002 TYR A 521 ARG 0.006 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.6758 (tmm) cc_final: 0.6123 (tmm) REVERT: A 620 MET cc_start: -0.3109 (tpp) cc_final: -0.3999 (mmt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2845 time to fit residues: 34.8353 Evaluate side-chains 66 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.5980 chunk 140 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 132 optimal weight: 40.0000 chunk 139 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4587 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14587 Z= 0.201 Angle : 0.631 8.859 20180 Z= 0.331 Chirality : 0.043 0.251 2344 Planarity : 0.004 0.064 2238 Dihedral : 16.991 83.201 3078 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -0.89 (0.22), residues: 1484 helix: 0.03 (0.19), residues: 685 sheet: -1.61 (0.41), residues: 146 loop : -0.90 (0.27), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 986 HIS 0.008 0.001 HIS A 803 PHE 0.023 0.002 PHE A1331 TYR 0.027 0.002 TYR A 521 ARG 0.004 0.000 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.6642 (tmm) cc_final: 0.5799 (tmm) REVERT: A 620 MET cc_start: -0.2966 (tpp) cc_final: -0.4034 (mmt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2886 time to fit residues: 33.6850 Evaluate side-chains 65 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 70 optimal weight: 0.0870 chunk 102 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 143 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 95 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4450 moved from start: 0.7005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14587 Z= 0.162 Angle : 0.621 12.119 20180 Z= 0.317 Chirality : 0.042 0.222 2344 Planarity : 0.004 0.064 2238 Dihedral : 16.770 83.370 3078 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -0.72 (0.22), residues: 1484 helix: 0.22 (0.20), residues: 675 sheet: -1.54 (0.39), residues: 165 loop : -0.81 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A 986 HIS 0.007 0.001 HIS A 803 PHE 0.021 0.001 PHE A1331 TYR 0.028 0.001 TYR A 521 ARG 0.004 0.000 ARG A 334 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.6541 (tmm) cc_final: 0.5727 (tmm) REVERT: A 244 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8678 (mttt) REVERT: A 620 MET cc_start: -0.2912 (tpp) cc_final: -0.3867 (mmt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3128 time to fit residues: 38.7113 Evaluate side-chains 69 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 127 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.079449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.060031 restraints weight = 154674.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.060031 restraints weight = 146645.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.060031 restraints weight = 146641.173| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14587 Z= 0.160 Angle : 0.607 8.967 20180 Z= 0.310 Chirality : 0.041 0.214 2344 Planarity : 0.004 0.065 2238 Dihedral : 16.697 82.043 3078 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.12 % Favored : 94.81 % 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: -0.61 (0.22), residues: 1484 helix: 0.25 (0.20), residues: 685 sheet: -1.36 (0.43), residues: 142 loop : -0.76 (0.27), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 986 HIS 0.005 0.001 HIS A 803 PHE 0.022 0.001 PHE A1331 TYR 0.025 0.001 TYR A 521 ARG 0.003 0.000 ARG A1418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2360.39 seconds wall clock time: 43 minutes 48.08 seconds (2628.08 seconds total)