Starting phenix.real_space_refine on Sat Mar 16 07:53:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0f_32241/03_2024/7w0f_32241.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0f_32241/03_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_32241/03_2024/7w0f_32241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0f_32241/03_2024/7w0f_32241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0f_32241/03_2024/7w0f_32241.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0f_32241/03_2024/7w0f_32241.pdb" } 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 Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1503": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.03, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 6.01 Conformation dependent library (CDL) restraints added in 2.2 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: 5.14 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: 7.52 Time building geometry restraints manager: 6.49 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: 94.32 - 102.27: 137 102.27 - 110.22: 3388 110.22 - 118.17: 8115 118.17 - 126.13: 8132 126.13 - 134.08: 408 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 2.520 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 ========== 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.660 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 45.600 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.510 ------------------------------------------------------------------------------- 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 : 1.525 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: 0.3172 time to fit residues: 83.8573 Evaluate side-chains 96 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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: 30.0000 chunk 118 optimal weight: 50.0000 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 HIS A 679 HIS A 815 HIS ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 HIS A1353 ASN A1385 HIS A1452 GLN ** A1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4228 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14587 Z= 0.277 Angle : 0.752 18.564 20180 Z= 0.383 Chirality : 0.044 0.326 2344 Planarity : 0.005 0.068 2238 Dihedral : 16.322 88.898 3078 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.74 % Rotamer: Outliers : 0.30 % Allowed : 6.40 % Favored : 93.30 % 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: -0.85 (0.22), residues: 1484 helix: 0.02 (0.20), residues: 674 sheet: -0.76 (0.38), residues: 156 loop : -1.03 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 986 HIS 0.006 0.001 HIS A 682 PHE 0.025 0.002 PHE A1387 TYR 0.028 0.002 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 111 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.657 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 104 ASP cc_start: 0.8441 (m-30) cc_final: 0.8077 (m-30) REVERT: A 208 MET cc_start: 0.6110 (tmm) cc_final: 0.5799 (tmm) REVERT: A 458 MET cc_start: -0.4169 (tpt) cc_final: -0.4705 (tpt) outliers start: 4 outliers final: 0 residues processed: 110 average time/residue: 0.3023 time to fit residues: 48.2467 Evaluate side-chains 78 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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: 20.0000 chunk 43 optimal weight: 0.0010 chunk 117 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 141 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- 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 490 GLN A1004 HIS ** A1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4245 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14587 Z= 0.198 Angle : 0.632 14.274 20180 Z= 0.321 Chirality : 0.041 0.174 2344 Planarity : 0.004 0.069 2238 Dihedral : 16.491 88.961 3078 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 0.15 % Allowed : 3.43 % Favored : 96.43 % 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: -0.76 (0.22), residues: 1484 helix: 0.10 (0.20), residues: 681 sheet: -0.97 (0.37), residues: 170 loop : -0.92 (0.27), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 986 HIS 0.008 0.001 HIS A 323 PHE 0.025 0.002 PHE A1387 TYR 0.019 0.002 TYR A1232 ARG 0.004 0.000 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 94 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.568 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 104 ASP cc_start: 0.8453 (m-30) cc_final: 0.8180 (p0) REVERT: A 241 GLU cc_start: 0.8150 (pm20) cc_final: 0.7371 (pm20) REVERT: A 458 MET cc_start: -0.4393 (tpt) cc_final: -0.4598 (tpt) REVERT: A 625 MET cc_start: 0.3709 (ptt) cc_final: 0.3387 (ptt) outliers start: 2 outliers final: 0 residues processed: 94 average time/residue: 0.3201 time to fit residues: 43.8300 Evaluate side-chains 75 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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: 30.0000 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 ** A1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4317 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14587 Z= 0.188 Angle : 0.622 11.328 20180 Z= 0.317 Chirality : 0.040 0.168 2344 Planarity : 0.004 0.063 2238 Dihedral : 16.539 91.740 3078 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 0.15 % Allowed : 4.62 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.22), residues: 1484 helix: 0.15 (0.20), residues: 679 sheet: -1.11 (0.37), residues: 165 loop : -0.94 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 986 HIS 0.006 0.001 HIS A 335 PHE 0.023 0.002 PHE A1387 TYR 0.016 0.002 TYR A1232 ARG 0.004 0.000 ARG A 602 *********************** 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 90 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 1.589 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: A 104 ASP cc_start: 0.8382 (m-30) cc_final: 0.8140 (p0) REVERT: A 625 MET cc_start: 0.4172 (ptt) cc_final: 0.3961 (ptt) outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 0.3054 time to fit residues: 39.9396 Evaluate side-chains 75 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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: 9.9990 chunk 2 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 0.0170 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 overall best weight: 3.4026 ------------------------------------------------------------------------------- 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 428 ASN ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4391 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14587 Z= 0.195 Angle : 0.612 8.115 20180 Z= 0.314 Chirality : 0.040 0.187 2344 Planarity : 0.004 0.057 2238 Dihedral : 16.616 90.299 3078 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.19), residues: 689 sheet: -1.12 (0.37), residues: 166 loop : -0.88 (0.27), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 986 HIS 0.005 0.001 HIS A 323 PHE 0.018 0.001 PHE A1387 TYR 0.014 0.002 TYR A1232 ARG 0.007 0.000 ARG A1418 *********************** 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 85 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.587 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 104 ASP cc_start: 0.8323 (m-30) cc_final: 0.8079 (p0) REVERT: A 241 GLU cc_start: 0.8403 (pm20) cc_final: 0.7819 (pm20) REVERT: A 458 MET cc_start: -0.3598 (mmm) cc_final: -0.4489 (mtp) REVERT: A 620 MET cc_start: -0.2400 (tpp) cc_final: -0.3778 (mmt) REVERT: A 625 MET cc_start: 0.3802 (ptt) cc_final: 0.3438 (ptt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3104 time to fit residues: 38.6895 Evaluate side-chains 74 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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: 8.9990 chunk 135 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 0.0000 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 HIS ** A1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4572 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14587 Z= 0.241 Angle : 0.667 8.059 20180 Z= 0.347 Chirality : 0.043 0.244 2344 Planarity : 0.005 0.124 2238 Dihedral : 16.832 88.541 3078 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 27.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.02 (0.19), residues: 697 sheet: -1.33 (0.37), residues: 166 loop : -1.01 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 986 HIS 0.011 0.002 HIS A 934 PHE 0.021 0.002 PHE A1331 TYR 0.018 0.002 TYR A1232 ARG 0.020 0.001 ARG A 627 *********************** 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: 0 poor density : 86 time to evaluate : 1.454 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 104 ASP cc_start: 0.8307 (m-30) cc_final: 0.8061 (p0) REVERT: A 222 MET cc_start: 0.7448 (tmm) cc_final: 0.7112 (tmm) REVERT: A 241 GLU cc_start: 0.8344 (pm20) cc_final: 0.8111 (pm20) REVERT: A 244 LYS cc_start: 0.9104 (mtmm) cc_final: 0.8902 (mttt) REVERT: A 458 MET cc_start: -0.2668 (mmm) cc_final: -0.3180 (mmt) REVERT: A 625 MET cc_start: 0.3859 (ptt) cc_final: 0.3018 (ptt) REVERT: A 908 MET cc_start: 0.6590 (mmp) cc_final: 0.6390 (mmp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3061 time to fit residues: 38.4661 Evaluate side-chains 70 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 127 optimal weight: 0.0000 chunk 84 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 chunk 69 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN ** A 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN ** A1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4464 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14587 Z= 0.172 Angle : 0.608 12.351 20180 Z= 0.309 Chirality : 0.041 0.185 2344 Planarity : 0.004 0.055 2238 Dihedral : 16.778 89.007 3078 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer: Outliers : 0.15 % Allowed : 1.71 % Favored : 98.14 % 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: -0.80 (0.22), residues: 1484 helix: 0.19 (0.19), residues: 691 sheet: -1.40 (0.38), residues: 161 loop : -0.97 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 986 HIS 0.008 0.001 HIS A 803 PHE 0.017 0.001 PHE A1387 TYR 0.017 0.001 TYR A1232 ARG 0.007 0.000 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 85 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 1.490 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: 0.7322 (tmm) cc_final: 0.6851 (tmm) REVERT: A 458 MET cc_start: -0.3324 (mmm) cc_final: -0.3530 (mmm) REVERT: A 625 MET cc_start: 0.3626 (ptt) cc_final: 0.3080 (ptt) outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 0.2921 time to fit residues: 36.7915 Evaluate side-chains 68 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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: 8.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 454 ASN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 ASN ** A1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4844 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14587 Z= 0.338 Angle : 0.803 10.267 20180 Z= 0.419 Chirality : 0.047 0.239 2344 Planarity : 0.006 0.066 2238 Dihedral : 17.339 85.338 3078 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 40.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.01 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -1.42 (0.21), residues: 1484 helix: -0.43 (0.18), residues: 690 sheet: -1.60 (0.37), residues: 167 loop : -1.18 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP A 986 HIS 0.009 0.003 HIS A 899 PHE 0.029 0.003 PHE A1393 TYR 0.023 0.003 TYR A 88 ARG 0.011 0.001 ARG A 943 *********************** 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 74 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.7452 (tmm) cc_final: 0.7150 (tmm) REVERT: A 458 MET cc_start: -0.2425 (mmm) cc_final: -0.2653 (mmt) REVERT: A 620 MET cc_start: -0.2594 (tpp) cc_final: -0.2932 (tpt) REVERT: A 625 MET cc_start: 0.4071 (ptt) cc_final: 0.3117 (ptt) REVERT: A 908 MET cc_start: 0.6813 (mmp) cc_final: 0.6128 (mmp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2872 time to fit residues: 31.9983 Evaluate side-chains 60 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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: 7.9990 chunk 140 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 92 optimal weight: 0.0370 overall best weight: 3.5864 ------------------------------------------------------------------------------- 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 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4713 moved from start: 0.7692 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= 0.210 Angle : 0.672 8.984 20180 Z= 0.346 Chirality : 0.043 0.178 2344 Planarity : 0.004 0.053 2238 Dihedral : 17.280 87.616 3078 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 27.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.60 % 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: -1.19 (0.22), residues: 1484 helix: -0.19 (0.19), residues: 690 sheet: -1.69 (0.38), residues: 156 loop : -1.08 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 986 HIS 0.007 0.001 HIS A1004 PHE 0.018 0.002 PHE A1387 TYR 0.018 0.002 TYR A1232 ARG 0.006 0.001 ARG A 627 *********************** 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 75 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.7373 (tmm) cc_final: 0.6810 (tmm) REVERT: A 458 MET cc_start: -0.2807 (mmm) cc_final: -0.3096 (mmt) REVERT: A 625 MET cc_start: 0.3985 (ptt) cc_final: 0.3054 (ptt) REVERT: A 908 MET cc_start: 0.6361 (mmp) cc_final: 0.6030 (mmp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2774 time to fit residues: 31.8630 Evaluate side-chains 56 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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: 0.9990 chunk 70 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 30.0000 chunk 143 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 12 optimal weight: 30.0000 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 142 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4714 moved from start: 0.7871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14587 Z= 0.207 Angle : 0.663 10.000 20180 Z= 0.340 Chirality : 0.042 0.184 2344 Planarity : 0.004 0.054 2238 Dihedral : 17.211 85.951 3078 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 27.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.40 % Favored : 93.53 % 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: -1.19 (0.22), residues: 1484 helix: -0.18 (0.19), residues: 696 sheet: -1.69 (0.38), residues: 155 loop : -1.12 (0.27), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 986 HIS 0.006 0.001 HIS A1004 PHE 0.026 0.002 PHE A 818 TYR 0.018 0.002 TYR A 578 ARG 0.004 0.001 ARG A 627 ********************** 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 72 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.7438 (tmm) cc_final: 0.6895 (tmm) REVERT: A 625 MET cc_start: 0.3963 (ptt) cc_final: 0.3116 (ptt) REVERT: A 908 MET cc_start: 0.6701 (mmp) cc_final: 0.6139 (mmp) REVERT: A 1602 MET cc_start: -0.1815 (pmm) cc_final: -0.2060 (pmm) REVERT: A 1632 ARG cc_start: 0.7434 (mmm160) cc_final: 0.7198 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2694 time to fit residues: 30.2349 Evaluate side-chains 57 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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: 30.0000 chunk 37 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 342 GLN ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** 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 = 0.4293 r_free = 0.4293 target = 0.075237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.056603 restraints weight = 160744.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.055858 restraints weight = 165082.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.055953 restraints weight = 173999.940| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.7993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14587 Z= 0.188 Angle : 0.641 9.520 20180 Z= 0.328 Chirality : 0.042 0.176 2344 Planarity : 0.004 0.053 2238 Dihedral : 17.140 85.843 3078 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 0.07 % Allowed : 0.30 % Favored : 99.63 % 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: -1.02 (0.22), residues: 1484 helix: -0.01 (0.19), residues: 690 sheet: -1.65 (0.40), residues: 143 loop : -1.05 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 986 HIS 0.006 0.001 HIS A1004 PHE 0.028 0.002 PHE A 981 TYR 0.020 0.002 TYR A 402 ARG 0.003 0.000 ARG A 627 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.51 seconds wall clock time: 44 minutes 6.47 seconds (2646.47 seconds total)