Starting phenix.real_space_refine (version: dev) on Sun Feb 26 01:47:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0a_32236/02_2023/7w0a_32236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0a_32236/02_2023/7w0a_32236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0a_32236/02_2023/7w0a_32236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0a_32236/02_2023/7w0a_32236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0a_32236/02_2023/7w0a_32236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0a_32236/02_2023/7w0a_32236.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 sd= 0.103 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 Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A ASP 104": "OD1" <-> "OD2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ASP 527": "OD1" <-> "OD2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A TYR 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A PHE 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1034": "OE1" <-> "OE2" Residue "A ASP 1259": "OD1" <-> "OD2" Residue "A ASP 1261": "OD1" <-> "OD2" Residue "A GLU 1351": "OE1" <-> "OE2" Residue "A ASP 1368": "OD1" <-> "OD2" Residue "A GLU 1371": "OE1" <-> "OE2" Residue "A PHE 1488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1528": "OE1" <-> "OE2" Residue "A GLU 1534": "OE1" <-> "OE2" Residue "A GLU 1642": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E ASP 96": "OD1" <-> "OD2" Residue "E ASP 104": "OD1" <-> "OD2" Residue "E TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 356": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E GLU 510": "OE1" <-> "OE2" Residue "E ASP 527": "OD1" <-> "OD2" Residue "E ASP 554": "OD1" <-> "OD2" Residue "E GLU 736": "OE1" <-> "OE2" Residue "E TYR 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 794": "OE1" <-> "OE2" Residue "E TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 936": "OD1" <-> "OD2" Residue "E PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1034": "OE1" <-> "OE2" Residue "E ASP 1259": "OD1" <-> "OD2" Residue "E ASP 1261": "OD1" <-> "OD2" Residue "E GLU 1351": "OE1" <-> "OE2" Residue "E ASP 1368": "OD1" <-> "OD2" Residue "E GLU 1371": "OE1" <-> "OE2" Residue "E PHE 1488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1528": "OE1" <-> "OE2" Residue "E GLU 1534": "OE1" <-> "OE2" Residue "E GLU 1642": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26898 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1478, 11988 Classifications: {'peptide': 1478} Link IDs: {'PTRANS': 61, 'TRANS': 1416} Chain breaks: 2 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 645 Classifications: {'DNA': 1, 'RNA': 30} Modifications used: {'5*END': 1, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna3p': 30} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 672 Classifications: {'RNA': 32} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 19} Link IDs: {'rna3p': 31} Chain: "F" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "G" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 645 Classifications: {'DNA': 1, 'RNA': 30} Modifications used: {'5*END': 1, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna3p': 30} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 672 Classifications: {'RNA': 32} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 19} Link IDs: {'rna3p': 31} Chain: "E" Number of atoms: 11988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1478, 11988 Classifications: {'peptide': 1478} Link IDs: {'PTRANS': 61, 'TRANS': 1416} Chain breaks: 2 Time building chain proxies: 15.40, per 1000 atoms: 0.57 Number of scatterers: 26898 At special positions: 0 Unit cell: (243.843, 177.243, 97.7522, 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 124 16.00 P 124 15.00 O 5308 8.00 N 4598 7.00 C 16744 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: 12.33 Conformation dependent library (CDL) restraints added in 3.5 seconds 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 20 sheets defined 55.4% alpha, 10.0% beta 44 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 8.49 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.741A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 45 removed outlier: 3.752A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 89 through 97 removed outlier: 5.928A pdb=" N VAL A 94 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP A 95 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.573A pdb=" N GLU A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 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 156 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 161 through 165 removed outlier: 3.674A pdb=" N LYS A 164 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 165 " --> pdb=" O GLN A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 165' Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.686A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 232 through 250 removed outlier: 3.625A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 removed outlier: 3.655A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 removed outlier: 3.561A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.802A pdb=" N ASP A 348 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.875A pdb=" N GLU A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.778A pdb=" N ILE A 386 " --> pdb=" O PRO A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.633A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 510 through 535 Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.559A pdb=" N PHE A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 608 through 611 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.761A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 687 removed outlier: 3.732A pdb=" N LYS A 685 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 removed outlier: 3.706A pdb=" N ALA A 697 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.865A pdb=" N GLN A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.697A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 869 removed outlier: 4.333A pdb=" N GLN A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 869 " --> pdb=" O GLN A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.533A pdb=" N PHE A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 930 removed outlier: 6.708A pdb=" N ASN A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.919A pdb=" N MET A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 983 through 991 removed outlier: 4.027A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1016 removed outlier: 3.727A pdb=" N PHE A1001 " --> pdb=" O ASN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 removed outlier: 3.530A pdb=" N SER A1182 " --> pdb=" O GLN A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.879A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 Processing helix chain 'A' and resid 1249 through 1259 Processing helix chain 'A' and resid 1260 through 1261 No H-bonds generated for 'chain 'A' and resid 1260 through 1261' Processing helix chain 'A' and resid 1262 through 1266 removed outlier: 3.985A pdb=" N LEU A1266 " --> pdb=" O PRO A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 3.823A pdb=" N TRP A1277 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1294 Processing helix chain 'A' and resid 1303 through 1308 Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1337 Processing helix chain 'A' and resid 1338 through 1340 No H-bonds generated for 'chain 'A' and resid 1338 through 1340' Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1354 through 1356 No H-bonds generated for 'chain 'A' and resid 1354 through 1356' Processing helix chain 'A' and resid 1363 through 1393 removed outlier: 8.103A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1410 removed outlier: 3.561A pdb=" N LEU A1407 " --> pdb=" O LEU A1404 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A1408 " --> pdb=" O THR A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.985A pdb=" N ILE A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 3.761A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1507 Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1521 through 1525 removed outlier: 3.601A pdb=" N ILE A1525 " --> pdb=" O HIS A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1546 removed outlier: 3.508A pdb=" N GLN A1546 " --> pdb=" O PHE A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 4.172A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1649 Proline residue: A1643 - end of helix Processing helix chain 'E' and resid 9 through 22 removed outlier: 3.741A pdb=" N LYS E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 45 removed outlier: 3.773A pdb=" N THR E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 Processing helix chain 'E' and resid 66 through 81 Processing helix chain 'E' and resid 89 through 97 removed outlier: 5.927A pdb=" N VAL E 94 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP E 95 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 109 removed outlier: 3.561A pdb=" N GLU E 105 " --> pdb=" O MET E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 148 through 156 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.676A pdb=" N LYS E 164 " --> pdb=" O ASN E 161 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 161 through 165' Processing helix chain 'E' and resid 183 through 195 removed outlier: 3.691A pdb=" N LYS E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 212 Processing helix chain 'E' and resid 232 through 250 removed outlier: 3.625A pdb=" N ARG E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 292 removed outlier: 3.655A pdb=" N VAL E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 314 removed outlier: 3.553A pdb=" N ILE E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 343 Processing helix chain 'E' and resid 344 through 348 removed outlier: 3.804A pdb=" N ASP E 348 " --> pdb=" O THR E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 362 removed outlier: 3.886A pdb=" N GLU E 356 " --> pdb=" O ASN E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 378 Processing helix chain 'E' and resid 382 through 386 removed outlier: 3.778A pdb=" N ILE E 386 " --> pdb=" O PRO E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 410 removed outlier: 3.633A pdb=" N CYS E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS E 399 " --> pdb=" O ARG E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 452 Processing helix chain 'E' and resid 484 through 493 Processing helix chain 'E' and resid 510 through 535 Processing helix chain 'E' and resid 543 through 552 removed outlier: 3.575A pdb=" N PHE E 551 " --> pdb=" O ILE E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 569 No H-bonds generated for 'chain 'E' and resid 567 through 569' Processing helix chain 'E' and resid 570 through 580 Processing helix chain 'E' and resid 598 through 607 Processing helix chain 'E' and resid 608 through 611 Processing helix chain 'E' and resid 637 through 656 Processing helix chain 'E' and resid 667 through 680 removed outlier: 3.762A pdb=" N ILE E 675 " --> pdb=" O ARG E 671 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP E 677 " --> pdb=" O ALA E 673 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL E 678 " --> pdb=" O SER E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 687 removed outlier: 3.730A pdb=" N LYS E 685 " --> pdb=" O HIS E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 697 removed outlier: 3.709A pdb=" N ALA E 697 " --> pdb=" O VAL E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 749 removed outlier: 3.862A pdb=" N GLN E 749 " --> pdb=" O TYR E 745 " (cutoff:3.500A) Processing helix chain 'E' and resid 792 through 810 removed outlier: 3.695A pdb=" N PHE E 807 " --> pdb=" O HIS E 803 " (cutoff:3.500A) Processing helix chain 'E' and resid 845 through 852 removed outlier: 3.658A pdb=" N MET E 849 " --> pdb=" O ASP E 845 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 869 removed outlier: 4.333A pdb=" N GLN E 868 " --> pdb=" O GLN E 864 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN E 869 " --> pdb=" O GLN E 865 " (cutoff:3.500A) Processing helix chain 'E' and resid 873 through 878 removed outlier: 3.533A pdb=" N PHE E 877 " --> pdb=" O ARG E 873 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 930 removed outlier: 6.712A pdb=" N ASN E 927 " --> pdb=" O SER E 923 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG E 928 " --> pdb=" O LYS E 924 " (cutoff:3.500A) Processing helix chain 'E' and resid 960 through 967 removed outlier: 3.919A pdb=" N MET E 967 " --> pdb=" O SER E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 972 through 974 No H-bonds generated for 'chain 'E' and resid 972 through 974' Processing helix chain 'E' and resid 983 through 991 removed outlier: 4.019A pdb=" N PHE E 991 " --> pdb=" O LEU E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 991 through 1016 removed outlier: 3.727A pdb=" N PHE E1001 " --> pdb=" O ASN E 997 " (cutoff:3.500A) Processing helix chain 'E' and resid 1174 through 1182 removed outlier: 3.530A pdb=" N SER E1182 " --> pdb=" O GLN E1178 " (cutoff:3.500A) Processing helix chain 'E' and resid 1183 through 1186 Processing helix chain 'E' and resid 1190 through 1199 Processing helix chain 'E' and resid 1209 through 1232 removed outlier: 3.881A pdb=" N LEU E1215 " --> pdb=" O ARG E1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 1236 through 1248 Processing helix chain 'E' and resid 1249 through 1259 Processing helix chain 'E' and resid 1260 through 1261 No H-bonds generated for 'chain 'E' and resid 1260 through 1261' Processing helix chain 'E' and resid 1262 through 1266 removed outlier: 3.984A pdb=" N LEU E1266 " --> pdb=" O PRO E1263 " (cutoff:3.500A) Processing helix chain 'E' and resid 1272 through 1277 removed outlier: 3.822A pdb=" N TRP E1277 " --> pdb=" O PRO E1273 " (cutoff:3.500A) Processing helix chain 'E' and resid 1285 through 1294 Processing helix chain 'E' and resid 1303 through 1308 Processing helix chain 'E' and resid 1313 through 1319 Processing helix chain 'E' and resid 1324 through 1337 Processing helix chain 'E' and resid 1338 through 1340 No H-bonds generated for 'chain 'E' and resid 1338 through 1340' Processing helix chain 'E' and resid 1348 through 1353 Processing helix chain 'E' and resid 1354 through 1356 No H-bonds generated for 'chain 'E' and resid 1354 through 1356' Processing helix chain 'E' and resid 1363 through 1393 removed outlier: 8.111A pdb=" N LEU E1383 " --> pdb=" O LYS E1379 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N GLN E1384 " --> pdb=" O ASN E1380 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS E1385 " --> pdb=" O TYR E1381 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS E1388 " --> pdb=" O GLN E1384 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET E1389 " --> pdb=" O HIS E1385 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU E1390 " --> pdb=" O ALA E1386 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU E1391 " --> pdb=" O PHE E1387 " (cutoff:3.500A) Processing helix chain 'E' and resid 1403 through 1410 removed outlier: 3.563A pdb=" N LEU E1407 " --> pdb=" O LEU E1404 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU E1408 " --> pdb=" O THR E1405 " (cutoff:3.500A) Processing helix chain 'E' and resid 1422 through 1430 removed outlier: 3.986A pdb=" N ILE E1426 " --> pdb=" O ASN E1422 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE E1429 " --> pdb=" O GLU E1425 " (cutoff:3.500A) Processing helix chain 'E' and resid 1432 through 1441 Processing helix chain 'E' and resid 1447 through 1455 Processing helix chain 'E' and resid 1468 through 1491 removed outlier: 3.762A pdb=" N ILE E1474 " --> pdb=" O GLU E1470 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA E1477 " --> pdb=" O PHE E1473 " (cutoff:3.500A) Processing helix chain 'E' and resid 1495 through 1507 Processing helix chain 'E' and resid 1508 through 1519 Processing helix chain 'E' and resid 1521 through 1525 removed outlier: 3.599A pdb=" N ILE E1525 " --> pdb=" O HIS E1522 " (cutoff:3.500A) Processing helix chain 'E' and resid 1529 through 1546 removed outlier: 3.510A pdb=" N GLN E1546 " --> pdb=" O PHE E1542 " (cutoff:3.500A) Processing helix chain 'E' and resid 1609 through 1628 removed outlier: 4.177A pdb=" N GLY E1613 " --> pdb=" O PRO E1609 " (cutoff:3.500A) Processing helix chain 'E' and resid 1629 through 1649 Proline residue: E1643 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 5.822A pdb=" N GLY A 86 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR A 115 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR A 88 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG A 59 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 136 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 61 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE A 138 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET A 63 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 6.179A 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: 6.608A pdb=" N GLN A 422 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR A 219 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU A 504 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 221 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR A 506 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 223 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.658A pdb=" N ARG A 260 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 772 Processing sheet with id=AA8, first strand: chain 'A' and resid 768 through 772 removed outlier: 4.616A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AB1, first strand: chain 'A' and resid 969 through 971 removed outlier: 4.415A pdb=" N VAL A 969 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET A 939 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL A 898 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU A 941 " --> pdb=" O THR A 896 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS A 880 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 357 through 358 removed outlier: 6.232A pdb=" N THR E 219 " --> pdb=" O PHE E 502 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU E 504 " --> pdb=" O THR E 219 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL E 221 " --> pdb=" O LEU E 504 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR E 506 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL E 223 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU E 389 " --> pdb=" O PHE E 477 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN E 422 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 85 through 88 removed outlier: 5.825A pdb=" N GLY E 86 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N THR E 115 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR E 88 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG E 59 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL E 136 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU E 61 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE E 138 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET E 63 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE E 25 " --> pdb=" O ILE E 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 260 through 261 removed outlier: 4.659A pdb=" N ARG E 260 " --> pdb=" O ARG E 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AB6, first strand: chain 'E' and resid 593 through 596 Processing sheet with id=AB7, first strand: chain 'E' and resid 702 through 706 Processing sheet with id=AB8, first strand: chain 'E' and resid 768 through 772 Processing sheet with id=AB9, first strand: chain 'E' and resid 768 through 772 removed outlier: 4.620A pdb=" N TYR E 754 " --> pdb=" O ILE E 729 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 819 through 820 Processing sheet with id=AC2, first strand: chain 'E' and resid 969 through 971 removed outlier: 4.406A pdb=" N VAL E 969 " --> pdb=" O VAL E 942 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET E 939 " --> pdb=" O VAL E 898 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 898 " --> pdb=" O MET E 939 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLU E 941 " --> pdb=" O THR E 896 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS E 880 " --> pdb=" O VAL E 895 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE E 881 " --> pdb=" O PHE E 979 " (cutoff:3.500A) 1161 hydrogen bonds defined for protein. 3288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 15.69 Time building geometry restraints manager: 13.09 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: 7453 1.33 - 1.45: 5253 1.45 - 1.57: 14580 1.57 - 1.69: 246 1.69 - 1.81: 194 Bond restraints: 27726 Sorted by residual: bond pdb=" CB CYS E 400 " pdb=" SG CYS E 400 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.41e+00 bond pdb=" CB CYS A 400 " pdb=" SG CYS A 400 " ideal model delta sigma weight residual 1.808 1.770 0.038 3.30e-02 9.18e+02 1.35e+00 bond pdb=" CA SER E 461 " pdb=" CB SER E 461 " ideal model delta sigma weight residual 1.527 1.500 0.027 2.48e-02 1.63e+03 1.19e+00 bond pdb=" CA SER A 461 " pdb=" CB SER A 461 " ideal model delta sigma weight residual 1.527 1.500 0.027 2.48e-02 1.63e+03 1.19e+00 bond pdb=" CA MET A 967 " pdb=" CB MET A 967 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.41e-02 5.03e+03 1.16e+00 ... (remaining 27721 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.80: 1083 105.80 - 112.86: 14981 112.86 - 119.93: 9650 119.93 - 126.99: 11892 126.99 - 134.05: 502 Bond angle restraints: 38108 Sorted by residual: angle pdb=" CB MET A 360 " pdb=" CG MET A 360 " pdb=" SD MET A 360 " ideal model delta sigma weight residual 112.70 121.75 -9.05 3.00e+00 1.11e-01 9.11e+00 angle pdb=" C LYS A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.96e+00 angle pdb=" C LYS E 539 " pdb=" N THR E 540 " pdb=" CA THR E 540 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.57e+00 angle pdb=" C MET E 344 " pdb=" N THR E 345 " pdb=" CA THR E 345 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.41e+00 angle pdb=" C MET A 344 " pdb=" N THR A 345 " pdb=" CA THR A 345 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.39e+00 ... (remaining 38103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15003 17.98 - 35.95: 1223 35.95 - 53.93: 186 53.93 - 71.90: 48 71.90 - 89.88: 34 Dihedral angle restraints: 16494 sinusoidal: 7684 harmonic: 8810 Sorted by residual: dihedral pdb=" CA LEU E 758 " pdb=" C LEU E 758 " pdb=" N ARG E 759 " pdb=" CA ARG E 759 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N ARG A 759 " pdb=" CA ARG A 759 " ideal model delta harmonic sigma weight residual 180.00 161.60 18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASP E1261 " pdb=" CB ASP E1261 " pdb=" CG ASP E1261 " pdb=" OD1 ASP E1261 " ideal model delta sinusoidal sigma weight residual -30.00 -87.80 57.80 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 16491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3090 0.037 - 0.074: 937 0.074 - 0.111: 286 0.111 - 0.148: 57 0.148 - 0.184: 4 Chirality restraints: 4374 Sorted by residual: chirality pdb=" CB ILE B 344 " pdb=" CA ILE B 344 " pdb=" CG1 ILE B 344 " pdb=" CG2 ILE B 344 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CB VAL A 231 " pdb=" CA VAL A 231 " pdb=" CG1 VAL A 231 " pdb=" CG2 VAL A 231 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CB VAL E 231 " pdb=" CA VAL E 231 " pdb=" CG1 VAL E 231 " pdb=" CG2 VAL E 231 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 4371 not shown) Planarity restraints: 4426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 344 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C MET A 344 " 0.031 2.00e-02 2.50e+03 pdb=" O MET A 344 " -0.011 2.00e-02 2.50e+03 pdb=" N THR A 345 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A1456 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A1457 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1457 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1457 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 344 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C MET E 344 " 0.030 2.00e-02 2.50e+03 pdb=" O MET E 344 " -0.011 2.00e-02 2.50e+03 pdb=" N THR E 345 " -0.010 2.00e-02 2.50e+03 ... (remaining 4423 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1668 2.73 - 3.27: 27277 3.27 - 3.81: 45404 3.81 - 4.36: 55814 4.36 - 4.90: 91109 Nonbonded interactions: 221272 Sorted by model distance: nonbonded pdb=" O VAL E 437 " pdb=" NH1 ARG E 440 " model vdw 2.186 2.520 nonbonded pdb=" O VAL A 437 " pdb=" NH1 ARG A 440 " model vdw 2.195 2.520 nonbonded pdb=" NZ LYS A 340 " pdb=" OD1 ASP B 345 " model vdw 2.205 2.520 nonbonded pdb=" O2 C G 11 " pdb=" N2 G H 40 " model vdw 2.220 2.520 nonbonded pdb=" O2 C C 11 " pdb=" N2 G D 40 " model vdw 2.221 2.520 ... (remaining 221267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 124 5.49 5 S 124 5.16 5 C 16744 2.51 5 N 4598 2.21 5 O 5308 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.240 Check model and map are aligned: 0.400 Process input model: 81.600 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.004 0.039 27726 Z= 0.234 Angle : 0.525 9.054 38108 Z= 0.287 Chirality : 0.040 0.184 4374 Planarity : 0.004 0.056 4426 Dihedral : 13.552 89.877 10782 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.00 % 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: 0.62 (0.15), residues: 2972 helix: 1.04 (0.14), residues: 1416 sheet: -0.07 (0.31), residues: 302 loop : -0.05 (0.18), residues: 1254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 3.194 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.4258 time to fit residues: 224.5997 Evaluate side-chains 212 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.984 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 157 optimal weight: 50.0000 chunk 124 optimal weight: 0.6980 chunk 241 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1217 ASN A1306 ASN A1338 ASN ** A1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1469 GLN A1491 ASN E 800 HIS E1306 ASN E1338 ASN ** E1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1469 GLN E1491 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 27726 Z= 0.177 Angle : 0.494 5.747 38108 Z= 0.260 Chirality : 0.039 0.160 4374 Planarity : 0.004 0.055 4426 Dihedral : 5.067 51.196 4738 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2972 helix: 1.23 (0.14), residues: 1456 sheet: -0.33 (0.29), residues: 316 loop : 0.07 (0.18), residues: 1200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 3.175 Fit side-chains outliers start: 28 outliers final: 21 residues processed: 234 average time/residue: 0.4025 time to fit residues: 151.7304 Evaluate side-chains 207 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 3.150 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2461 time to fit residues: 14.0003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 0.0270 chunk 232 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 302 optimal weight: 0.5980 chunk 249 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 overall best weight: 2.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 27726 Z= 0.259 Angle : 0.507 5.693 38108 Z= 0.268 Chirality : 0.040 0.161 4374 Planarity : 0.004 0.044 4426 Dihedral : 5.112 50.219 4738 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.15), residues: 2972 helix: 1.13 (0.14), residues: 1450 sheet: -0.58 (0.27), residues: 332 loop : -0.00 (0.18), residues: 1190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 2.985 Fit side-chains outliers start: 20 outliers final: 7 residues processed: 205 average time/residue: 0.4053 time to fit residues: 135.2302 Evaluate side-chains 192 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 185 time to evaluate : 3.010 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3688 time to fit residues: 8.4103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 281 optimal weight: 8.9990 chunk 297 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 27726 Z= 0.239 Angle : 0.484 5.540 38108 Z= 0.256 Chirality : 0.039 0.172 4374 Planarity : 0.004 0.045 4426 Dihedral : 5.100 52.445 4738 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.67 % 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: 0.62 (0.15), residues: 2972 helix: 1.16 (0.14), residues: 1442 sheet: -0.69 (0.27), residues: 330 loop : -0.04 (0.18), residues: 1200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 2.915 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 211 average time/residue: 0.3999 time to fit residues: 138.5395 Evaluate side-chains 195 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 3.040 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2777 time to fit residues: 7.7932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 254 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 267 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 27726 Z= 0.260 Angle : 0.490 6.147 38108 Z= 0.260 Chirality : 0.040 0.180 4374 Planarity : 0.004 0.047 4426 Dihedral : 5.130 52.647 4738 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.89 % 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: 0.54 (0.15), residues: 2972 helix: 1.10 (0.14), residues: 1450 sheet: -0.79 (0.27), residues: 330 loop : -0.07 (0.18), residues: 1192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 3.260 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 217 average time/residue: 0.4080 time to fit residues: 144.9944 Evaluate side-chains 197 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 2.689 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2751 time to fit residues: 8.9458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 247 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 27726 Z= 0.238 Angle : 0.478 6.378 38108 Z= 0.254 Chirality : 0.039 0.173 4374 Planarity : 0.004 0.047 4426 Dihedral : 5.108 53.304 4738 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 2972 helix: 1.10 (0.14), residues: 1454 sheet: -0.84 (0.28), residues: 322 loop : -0.08 (0.18), residues: 1196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 3.083 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 205 average time/residue: 0.3957 time to fit residues: 134.2623 Evaluate side-chains 195 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 2.791 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2547 time to fit residues: 7.2721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 169 optimal weight: 0.1980 chunk 217 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 166 optimal weight: 0.0170 chunk 296 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 27726 Z= 0.139 Angle : 0.435 6.076 38108 Z= 0.231 Chirality : 0.037 0.179 4374 Planarity : 0.003 0.045 4426 Dihedral : 4.952 54.029 4738 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 2972 helix: 1.27 (0.14), residues: 1470 sheet: -0.73 (0.28), residues: 312 loop : -0.01 (0.18), residues: 1190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 3.387 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 208 average time/residue: 0.3908 time to fit residues: 133.7778 Evaluate side-chains 193 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 187 time to evaluate : 2.942 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2472 time to fit residues: 6.9069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 233 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 27726 Z= 0.283 Angle : 0.501 7.224 38108 Z= 0.264 Chirality : 0.040 0.169 4374 Planarity : 0.004 0.046 4426 Dihedral : 5.120 52.973 4738 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.78 % 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: 0.54 (0.15), residues: 2972 helix: 1.10 (0.14), residues: 1454 sheet: -0.88 (0.27), residues: 322 loop : -0.06 (0.18), residues: 1196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 188 time to evaluate : 2.899 Fit side-chains outliers start: 21 outliers final: 7 residues processed: 204 average time/residue: 0.4018 time to fit residues: 134.3687 Evaluate side-chains 192 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 185 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2512 time to fit residues: 7.3692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 259 optimal weight: 0.7980 chunk 276 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 249 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 27726 Z= 0.149 Angle : 0.448 5.781 38108 Z= 0.236 Chirality : 0.037 0.162 4374 Planarity : 0.003 0.044 4426 Dihedral : 4.972 54.390 4738 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.19 % 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: 0.71 (0.16), residues: 2972 helix: 1.24 (0.14), residues: 1470 sheet: -0.78 (0.28), residues: 312 loop : -0.01 (0.18), residues: 1190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 191 time to evaluate : 3.013 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 193 average time/residue: 0.4011 time to fit residues: 126.7562 Evaluate side-chains 189 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2398 time to fit residues: 4.6497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 9.9990 chunk 292 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 203 optimal weight: 0.4980 chunk 306 optimal weight: 3.9990 chunk 282 optimal weight: 8.9990 chunk 244 optimal weight: 0.0470 chunk 25 optimal weight: 0.0980 chunk 188 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 27726 Z= 0.122 Angle : 0.432 8.579 38108 Z= 0.228 Chirality : 0.036 0.163 4374 Planarity : 0.003 0.043 4426 Dihedral : 4.861 54.024 4738 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.11 % 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 (0.16), residues: 2972 helix: 1.50 (0.14), residues: 1436 sheet: -0.72 (0.27), residues: 320 loop : 0.09 (0.18), residues: 1216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 218 time to evaluate : 3.338 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 220 average time/residue: 0.3974 time to fit residues: 143.5686 Evaluate side-chains 199 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 3.245 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3579 time to fit residues: 5.0942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 5.9990 chunk 260 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 251 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.0030 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1287 ASN ** A1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1287 ASN ** E1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103350 restraints weight = 35450.537| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.11 r_work: 0.3142 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.058 27726 Z= 0.160 Angle : 0.453 7.350 38108 Z= 0.238 Chirality : 0.037 0.167 4374 Planarity : 0.003 0.043 4426 Dihedral : 4.897 53.574 4738 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.22 % 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 (0.16), residues: 2972 helix: 1.48 (0.14), residues: 1438 sheet: -0.68 (0.28), residues: 320 loop : 0.11 (0.18), residues: 1214 =============================================================================== Job complete usr+sys time: 5107.59 seconds wall clock time: 95 minutes 7.33 seconds (5707.33 seconds total)