Starting phenix.real_space_refine on Sun Jul 5 09:16:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w0a_32236/07_2026/7w0a_32236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0a_32236/07_2026/7w0a_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 { model { file = "/net/cci-nas-00/data/ceres_data/7w0a_32236/07_2026/7w0a_32236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0a_32236/07_2026/7w0a_32236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w0a_32236/07_2026/7w0a_32236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0a_32236/07_2026/7w0a_32236.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7w0a_32236/07_2026/7w0a_32236.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w0a_32236/07_2026/7w0a_32236.cif" } 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 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= 0.003 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 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. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 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: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 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: 6.15, per 1000 atoms: 0.23 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.0 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: 3.70 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: 7.64 Time building geometry restraints manager: 3.19 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: 0.00 - 1.81: 37591 1.81 - 3.62: 463 3.62 - 5.43: 47 5.43 - 7.24: 6 7.24 - 9.05: 1 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 3.120 nonbonded pdb=" O VAL A 437 " pdb=" NH1 ARG A 440 " model vdw 2.195 3.120 nonbonded pdb=" NZ LYS A 340 " pdb=" OD1 ASP B 345 " model vdw 2.205 3.120 nonbonded pdb=" O2 C G 11 " pdb=" N2 G H 40 " model vdw 2.220 3.120 nonbonded pdb=" O2 C C 11 " pdb=" N2 G D 40 " model vdw 2.221 3.120 ... (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 Time spend for trying shortcut: 0.05 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 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.250 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.240 ------------------------------------------------------------------------------- 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= 0.158 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 % Allowed : 0.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 764 TYR 0.017 0.001 TYR A1468 PHE 0.026 0.002 PHE E 818 TRP 0.020 0.002 TRP A1235 HIS 0.008 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (27726) covalent geometry : angle 0.52511 / 0.29 (38108) hydrogen bonds : bond 0.17092 / 11.21 ( 1247) hydrogen bonds : angle 6.87431 / 4.93 ( 3500) *********************** 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 to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.985 Fit side-chains REVERT: A 214 TYR cc_start: 0.8800 (p90) cc_final: 0.8153 (p90) REVERT: A 324 ARG cc_start: 0.6857 (mmm160) cc_final: 0.6650 (ttm-80) REVERT: A 527 ASP cc_start: 0.8056 (m-30) cc_final: 0.7697 (m-30) REVERT: A 548 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8118 (tptp) REVERT: E 324 ARG cc_start: 0.6861 (mmm160) cc_final: 0.6656 (ttm-80) REVERT: E 342 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7379 (mt0) REVERT: E 362 PHE cc_start: 0.8852 (m-80) cc_final: 0.8441 (m-10) REVERT: E 527 ASP cc_start: 0.8056 (m-30) cc_final: 0.7697 (m-30) REVERT: E 548 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8135 (tptp) REVERT: E 920 PHE cc_start: 0.8460 (t80) cc_final: 0.8228 (t80) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1660 time to fit residues: 88.4942 Evaluate side-chains 221 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0040 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1217 ASN A1491 ASN E 800 HIS E1491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.149250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104158 restraints weight = 35806.480| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.14 r_work: 0.3125 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27726 Z= 0.116 Angle : 0.499 5.582 38108 Z= 0.264 Chirality : 0.039 0.161 4374 Planarity : 0.004 0.040 4426 Dihedral : 5.098 51.619 4738 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.08 % Allowed : 6.10 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 2972 helix: 1.21 (0.14), residues: 1454 sheet: -0.42 (0.29), residues: 320 loop : 0.09 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.017 0.001 TYR E1000 PHE 0.015 0.001 PHE E 818 TRP 0.010 0.001 TRP E 986 HIS 0.003 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (27726) covalent geometry : angle 0.49915 / 0.26 (38108) hydrogen bonds : bond 0.04420 / 2.97 ( 1247) hydrogen bonds : angle 4.40076 / 3.15 ( 3500) *********************** 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 262 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.959 Fit side-chains REVERT: A 102 TRP cc_start: 0.8475 (m100) cc_final: 0.8039 (m100) REVERT: A 106 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8318 (mp) REVERT: A 214 TYR cc_start: 0.8833 (p90) cc_final: 0.8124 (p90) REVERT: A 527 ASP cc_start: 0.8399 (m-30) cc_final: 0.7927 (m-30) REVERT: A 548 LYS cc_start: 0.8352 (ttpt) cc_final: 0.7800 (tptp) REVERT: A 552 GLN cc_start: 0.7641 (pp30) cc_final: 0.7182 (pp30) REVERT: A 794 GLU cc_start: 0.8331 (pm20) cc_final: 0.7860 (tp30) REVERT: A 873 ARG cc_start: 0.8286 (mpp80) cc_final: 0.7988 (ptp-170) REVERT: A 1493 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8538 (mtmt) REVERT: B 352 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8413 (mtpt) REVERT: E 102 TRP cc_start: 0.8479 (m100) cc_final: 0.8046 (m100) REVERT: E 360 MET cc_start: 0.8471 (mmt) cc_final: 0.8138 (mmm) REVERT: E 527 ASP cc_start: 0.8413 (m-30) cc_final: 0.7936 (m-30) REVERT: E 548 LYS cc_start: 0.8336 (ttpt) cc_final: 0.7757 (tptp) REVERT: E 794 GLU cc_start: 0.8302 (pm20) cc_final: 0.7848 (tp30) REVERT: E 873 ARG cc_start: 0.8270 (mpp80) cc_final: 0.7974 (ptp-170) REVERT: E 1493 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8537 (mtmt) outliers start: 29 outliers final: 18 residues processed: 250 average time/residue: 0.1755 time to fit residues: 70.6679 Evaluate side-chains 220 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1314 ASP Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 1038 SER Chi-restraints excluded: chain E residue 1314 ASP Chi-restraints excluded: chain E residue 1400 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 129 optimal weight: 7.9990 chunk 305 optimal weight: 4.9990 chunk 110 optimal weight: 0.4980 chunk 116 optimal weight: 6.9990 chunk 304 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 234 optimal weight: 0.3980 chunk 217 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100046 restraints weight = 35631.583| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.40 r_work: 0.3056 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27726 Z= 0.142 Angle : 0.494 6.037 38108 Z= 0.262 Chirality : 0.040 0.155 4374 Planarity : 0.004 0.042 4426 Dihedral : 5.065 50.102 4738 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.12 % Allowed : 8.14 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.15), residues: 2972 helix: 1.15 (0.14), residues: 1452 sheet: -0.57 (0.28), residues: 322 loop : 0.04 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.020 0.001 TYR E1000 PHE 0.018 0.001 PHE E1542 TRP 0.009 0.001 TRP E 986 HIS 0.004 0.001 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (27726) covalent geometry : angle 0.49426 / 0.26 (38108) hydrogen bonds : bond 0.04280 / 2.91 ( 1247) hydrogen bonds : angle 4.19566 / 3.00 ( 3500) *********************** 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 237 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.842 Fit side-chains REVERT: A 102 TRP cc_start: 0.8494 (m100) cc_final: 0.8123 (m100) REVERT: A 106 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8494 (mp) REVERT: A 527 ASP cc_start: 0.8542 (m-30) cc_final: 0.8048 (m-30) REVERT: A 548 LYS cc_start: 0.8396 (ttpt) cc_final: 0.7839 (tptp) REVERT: A 794 GLU cc_start: 0.8329 (pm20) cc_final: 0.7896 (tp30) REVERT: A 873 ARG cc_start: 0.8303 (mpp80) cc_final: 0.8000 (ptp-170) REVERT: A 1493 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8542 (mtmt) REVERT: A 1534 GLU cc_start: 0.7562 (tt0) cc_final: 0.7278 (tt0) REVERT: B 352 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8528 (mtpt) REVERT: E 527 ASP cc_start: 0.8543 (m-30) cc_final: 0.8048 (m-30) REVERT: E 548 LYS cc_start: 0.8394 (ttpt) cc_final: 0.7836 (tptp) REVERT: E 794 GLU cc_start: 0.8323 (pm20) cc_final: 0.7901 (tp30) REVERT: E 873 ARG cc_start: 0.8290 (mpp80) cc_final: 0.7983 (ptp-170) REVERT: E 1493 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8544 (mtmt) outliers start: 30 outliers final: 16 residues processed: 228 average time/residue: 0.1657 time to fit residues: 61.9215 Evaluate side-chains 210 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 1038 SER Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 216 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 158 optimal weight: 50.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097790 restraints weight = 35536.100| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.34 r_work: 0.3023 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27726 Z= 0.184 Angle : 0.518 5.798 38108 Z= 0.275 Chirality : 0.041 0.189 4374 Planarity : 0.004 0.045 4426 Dihedral : 5.220 51.939 4738 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.26 % Allowed : 9.81 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 2972 helix: 1.04 (0.14), residues: 1442 sheet: -0.68 (0.27), residues: 330 loop : -0.05 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 346 TYR 0.021 0.002 TYR E1000 PHE 0.013 0.001 PHE A1481 TRP 0.010 0.001 TRP E 986 HIS 0.007 0.001 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.18 (27726) covalent geometry : angle 0.51833 / 0.27 (38108) hydrogen bonds : bond 0.04470 / 3.05 ( 1247) hydrogen bonds : angle 4.25220 / 3.04 ( 3500) *********************** 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 238 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.978 Fit side-chains REVERT: A 102 TRP cc_start: 0.8522 (m100) cc_final: 0.8161 (m100) REVERT: A 106 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8482 (mp) REVERT: A 527 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: A 548 LYS cc_start: 0.8398 (ttpt) cc_final: 0.7820 (tptp) REVERT: A 794 GLU cc_start: 0.8364 (pm20) cc_final: 0.7988 (tp30) REVERT: A 873 ARG cc_start: 0.8229 (mpp80) cc_final: 0.7915 (ptp-170) REVERT: A 954 HIS cc_start: 0.7684 (t-90) cc_final: 0.7421 (t-90) REVERT: A 1493 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8508 (mtmt) REVERT: A 1534 GLU cc_start: 0.7527 (tt0) cc_final: 0.7247 (tt0) REVERT: E 102 TRP cc_start: 0.8488 (m100) cc_final: 0.8158 (m100) REVERT: E 344 MET cc_start: 0.6688 (ttp) cc_final: 0.5970 (ttp) REVERT: E 527 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: E 548 LYS cc_start: 0.8415 (ttpt) cc_final: 0.7863 (tptp) REVERT: E 794 GLU cc_start: 0.8386 (pm20) cc_final: 0.8022 (tp30) REVERT: E 800 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.8045 (t-90) REVERT: E 821 ASP cc_start: 0.8379 (t0) cc_final: 0.8112 (t70) REVERT: E 873 ARG cc_start: 0.8216 (mpp80) cc_final: 0.7900 (ptp-170) REVERT: E 1493 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8507 (mtmt) outliers start: 34 outliers final: 17 residues processed: 230 average time/residue: 0.1738 time to fit residues: 64.8402 Evaluate side-chains 218 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 800 HIS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 168 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.148997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102751 restraints weight = 35488.336| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.12 r_work: 0.3127 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27726 Z= 0.102 Angle : 0.448 5.750 38108 Z= 0.239 Chirality : 0.038 0.172 4374 Planarity : 0.003 0.043 4426 Dihedral : 5.007 53.646 4738 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.08 % Allowed : 10.97 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.15), residues: 2972 helix: 1.21 (0.14), residues: 1462 sheet: -0.69 (0.28), residues: 320 loop : 0.05 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 346 TYR 0.014 0.001 TYR E 740 PHE 0.019 0.001 PHE E1542 TRP 0.010 0.001 TRP A1634 HIS 0.002 0.000 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (27726) covalent geometry : angle 0.44762 / 0.24 (38108) hydrogen bonds : bond 0.03625 / 2.47 ( 1247) hydrogen bonds : angle 3.99675 / 2.85 ( 3500) *********************** 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 245 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 1.074 Fit side-chains REVERT: A 102 TRP cc_start: 0.8442 (m100) cc_final: 0.8218 (m100) REVERT: A 527 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8143 (m-30) REVERT: A 548 LYS cc_start: 0.8419 (ttpt) cc_final: 0.7868 (tptp) REVERT: A 794 GLU cc_start: 0.8282 (pm20) cc_final: 0.8009 (tp30) REVERT: A 821 ASP cc_start: 0.8299 (t70) cc_final: 0.7877 (t0) REVERT: A 873 ARG cc_start: 0.8235 (mpp80) cc_final: 0.7929 (ptp-170) REVERT: A 918 TYR cc_start: 0.8419 (t80) cc_final: 0.8148 (t80) REVERT: A 1493 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8541 (mtmt) REVERT: E 344 MET cc_start: 0.6723 (ttp) cc_final: 0.6043 (ttp) REVERT: E 527 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: E 548 LYS cc_start: 0.8460 (ttpt) cc_final: 0.7907 (tptp) REVERT: E 794 GLU cc_start: 0.8323 (pm20) cc_final: 0.8090 (tp30) REVERT: E 873 ARG cc_start: 0.8229 (mpp80) cc_final: 0.7924 (ptp-170) REVERT: E 918 TYR cc_start: 0.8423 (t80) cc_final: 0.8147 (t80) REVERT: E 1493 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8529 (mtmt) outliers start: 29 outliers final: 14 residues processed: 233 average time/residue: 0.1809 time to fit residues: 68.7531 Evaluate side-chains 214 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 120 optimal weight: 6.9990 chunk 301 optimal weight: 7.9990 chunk 193 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 189 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 157 optimal weight: 50.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.099694 restraints weight = 35441.721| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.11 r_work: 0.3081 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2360 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= 0.163 Angle : 0.493 6.191 38108 Z= 0.261 Chirality : 0.040 0.177 4374 Planarity : 0.004 0.046 4426 Dihedral : 5.108 52.466 4738 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.34 % Allowed : 11.19 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 2972 helix: 1.13 (0.14), residues: 1442 sheet: -0.80 (0.27), residues: 330 loop : -0.01 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 346 TYR 0.020 0.001 TYR E1000 PHE 0.012 0.001 PHE A1481 TRP 0.009 0.001 TRP A1634 HIS 0.004 0.001 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (27726) covalent geometry : angle 0.49277 / 0.26 (38108) hydrogen bonds : bond 0.04159 / 2.84 ( 1247) hydrogen bonds : angle 4.12591 / 2.94 ( 3500) *********************** 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 242 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 1.027 Fit side-chains REVERT: A 102 TRP cc_start: 0.8529 (m100) cc_final: 0.8279 (m100) REVERT: A 527 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: A 548 LYS cc_start: 0.8468 (ttpt) cc_final: 0.7904 (tptp) REVERT: A 794 GLU cc_start: 0.8317 (pm20) cc_final: 0.8083 (tp30) REVERT: A 873 ARG cc_start: 0.8264 (mpp80) cc_final: 0.7941 (ptp-170) REVERT: A 918 TYR cc_start: 0.8430 (t80) cc_final: 0.8165 (t80) REVERT: A 1493 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8569 (mtmt) REVERT: A 1534 GLU cc_start: 0.7635 (tt0) cc_final: 0.7358 (tt0) REVERT: E 102 TRP cc_start: 0.8514 (m100) cc_final: 0.8199 (m100) REVERT: E 527 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: E 548 LYS cc_start: 0.8496 (ttpt) cc_final: 0.7983 (tptp) REVERT: E 794 GLU cc_start: 0.8348 (pm20) cc_final: 0.8106 (tp30) REVERT: E 800 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8118 (t-90) REVERT: E 873 ARG cc_start: 0.8257 (mpp80) cc_final: 0.7935 (ptp-170) REVERT: E 918 TYR cc_start: 0.8373 (t80) cc_final: 0.8152 (t80) outliers start: 36 outliers final: 20 residues processed: 230 average time/residue: 0.1579 time to fit residues: 59.2503 Evaluate side-chains 217 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 800 HIS Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 166 optimal weight: 0.4980 chunk 303 optimal weight: 0.0050 chunk 292 optimal weight: 4.9990 chunk 263 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 208 optimal weight: 0.2980 chunk 223 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.151440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105568 restraints weight = 35323.607| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.23 r_work: 0.3153 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2489 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= 0.089 Angle : 0.438 6.583 38108 Z= 0.233 Chirality : 0.037 0.156 4374 Planarity : 0.003 0.043 4426 Dihedral : 4.937 53.890 4738 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.34 % Allowed : 11.49 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 2972 helix: 1.31 (0.14), residues: 1456 sheet: -0.67 (0.28), residues: 312 loop : 0.02 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 346 TYR 0.014 0.001 TYR E1624 PHE 0.018 0.001 PHE A1542 TRP 0.011 0.001 TRP A1634 HIS 0.001 0.000 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (27726) covalent geometry : angle 0.43829 / 0.23 (38108) hydrogen bonds : bond 0.03381 / 2.30 ( 1247) hydrogen bonds : angle 3.90724 / 2.78 ( 3500) *********************** 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 245 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.957 Fit side-chains REVERT: A 527 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: A 548 LYS cc_start: 0.8422 (ttpt) cc_final: 0.7861 (tptp) REVERT: A 794 GLU cc_start: 0.8234 (pm20) cc_final: 0.7992 (tp30) REVERT: A 821 ASP cc_start: 0.8245 (t70) cc_final: 0.7781 (t0) REVERT: A 873 ARG cc_start: 0.8266 (mpp80) cc_final: 0.7994 (mpp80) REVERT: A 918 TYR cc_start: 0.8390 (t80) cc_final: 0.8176 (t80) REVERT: E 527 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: E 548 LYS cc_start: 0.8432 (ttpt) cc_final: 0.7928 (tptp) REVERT: E 552 GLN cc_start: 0.7827 (pp30) cc_final: 0.7399 (pp30) REVERT: E 794 GLU cc_start: 0.8272 (pm20) cc_final: 0.8041 (tp30) REVERT: E 873 ARG cc_start: 0.8247 (mpp80) cc_final: 0.7822 (mpp80) REVERT: E 876 ASP cc_start: 0.8595 (m-30) cc_final: 0.8076 (m-30) REVERT: E 918 TYR cc_start: 0.8380 (t80) cc_final: 0.8161 (t80) outliers start: 36 outliers final: 21 residues processed: 232 average time/residue: 0.1714 time to fit residues: 65.9198 Evaluate side-chains 223 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1314 ASP Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 972 ILE Chi-restraints excluded: chain E residue 1482 LEU Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 303 optimal weight: 0.0870 chunk 187 optimal weight: 6.9990 chunk 259 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 243 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101464 restraints weight = 35466.574| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.22 r_work: 0.3098 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2496 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= 0.146 Angle : 0.480 6.542 38108 Z= 0.254 Chirality : 0.039 0.167 4374 Planarity : 0.004 0.045 4426 Dihedral : 5.047 53.006 4738 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.38 % Allowed : 11.64 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.15), residues: 2972 helix: 1.23 (0.14), residues: 1448 sheet: -0.77 (0.28), residues: 320 loop : -0.02 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 346 TYR 0.020 0.001 TYR E1000 PHE 0.010 0.001 PHE E1001 TRP 0.019 0.001 TRP A 102 HIS 0.003 0.001 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (27726) covalent geometry : angle 0.47969 / 0.25 (38108) hydrogen bonds : bond 0.03942 / 2.70 ( 1247) hydrogen bonds : angle 4.02675 / 2.87 ( 3500) *********************** 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 235 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.827 Fit side-chains REVERT: A 527 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: A 548 LYS cc_start: 0.8459 (ttpt) cc_final: 0.7885 (tptp) REVERT: A 794 GLU cc_start: 0.8358 (pm20) cc_final: 0.8107 (tp30) REVERT: A 873 ARG cc_start: 0.8292 (mpp80) cc_final: 0.8025 (mpp80) REVERT: A 908 MET cc_start: 0.5747 (mtt) cc_final: 0.5517 (mtt) REVERT: A 918 TYR cc_start: 0.8374 (t80) cc_final: 0.8136 (t80) REVERT: E 527 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: E 548 LYS cc_start: 0.8470 (ttpt) cc_final: 0.7948 (tptp) REVERT: E 794 GLU cc_start: 0.8356 (pm20) cc_final: 0.8108 (tp30) REVERT: E 873 ARG cc_start: 0.8268 (mpp80) cc_final: 0.8002 (mpp80) REVERT: E 918 TYR cc_start: 0.8407 (t80) cc_final: 0.8189 (t80) outliers start: 37 outliers final: 26 residues processed: 225 average time/residue: 0.1668 time to fit residues: 61.8229 Evaluate side-chains 220 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 1314 ASP Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 1356 VAL Chi-restraints excluded: chain E residue 1400 ILE Chi-restraints excluded: chain E residue 1482 LEU Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 274 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 164 optimal weight: 0.0770 chunk 241 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 5 optimal weight: 0.4980 chunk 94 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 overall best weight: 0.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103077 restraints weight = 35626.593| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.14 r_work: 0.3126 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27726 Z= 0.100 Angle : 0.447 6.123 38108 Z= 0.237 Chirality : 0.037 0.159 4374 Planarity : 0.003 0.044 4426 Dihedral : 4.971 54.078 4738 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.26 % Allowed : 11.78 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 2972 helix: 1.35 (0.14), residues: 1444 sheet: -0.71 (0.28), residues: 312 loop : -0.01 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 346 TYR 0.014 0.001 TYR E1000 PHE 0.018 0.001 PHE E1542 TRP 0.015 0.001 TRP A 102 HIS 0.002 0.001 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (27726) covalent geometry : angle 0.44663 / 0.24 (38108) hydrogen bonds : bond 0.03513 / 2.40 ( 1247) hydrogen bonds : angle 3.91044 / 2.79 ( 3500) *********************** 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 234 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.930 Fit side-chains REVERT: A 527 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: A 548 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7853 (tptp) REVERT: A 794 GLU cc_start: 0.8306 (pm20) cc_final: 0.8024 (tp30) REVERT: A 821 ASP cc_start: 0.8327 (t70) cc_final: 0.7947 (t70) REVERT: A 873 ARG cc_start: 0.8282 (mpp80) cc_final: 0.8011 (mpp80) REVERT: A 918 TYR cc_start: 0.8365 (t80) cc_final: 0.8152 (t80) REVERT: E 102 TRP cc_start: 0.8373 (m100) cc_final: 0.8032 (m100) REVERT: E 527 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8145 (m-30) REVERT: E 548 LYS cc_start: 0.8439 (ttpt) cc_final: 0.7930 (tptp) REVERT: E 552 GLN cc_start: 0.7780 (pp30) cc_final: 0.7339 (pp30) REVERT: E 794 GLU cc_start: 0.8318 (pm20) cc_final: 0.8047 (tp30) REVERT: E 873 ARG cc_start: 0.8277 (mpp80) cc_final: 0.8012 (mpp80) REVERT: E 918 TYR cc_start: 0.8364 (t80) cc_final: 0.8159 (t80) REVERT: E 1213 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8047 (tm-30) outliers start: 34 outliers final: 29 residues processed: 224 average time/residue: 0.1764 time to fit residues: 65.0511 Evaluate side-chains 228 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 1314 ASP Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 497 THR Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 1269 ILE Chi-restraints excluded: chain E residue 1356 VAL Chi-restraints excluded: chain E residue 1400 ILE Chi-restraints excluded: chain E residue 1482 LEU Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 2.9990 chunk 157 optimal weight: 50.0000 chunk 272 optimal weight: 0.0980 chunk 175 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 274 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 201 optimal weight: 0.8980 chunk 217 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.151559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105879 restraints weight = 35657.581| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.11 r_work: 0.3174 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27726 Z= 0.085 Angle : 0.431 5.970 38108 Z= 0.228 Chirality : 0.037 0.160 4374 Planarity : 0.003 0.043 4426 Dihedral : 4.878 53.932 4738 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.12 % Allowed : 12.08 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 2972 helix: 1.46 (0.14), residues: 1444 sheet: -0.70 (0.28), residues: 318 loop : 0.08 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 346 TYR 0.013 0.001 TYR E1624 PHE 0.010 0.001 PHE E1488 TRP 0.016 0.001 TRP A 102 HIS 0.002 0.000 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 (27726) covalent geometry : angle 0.43053 / 0.23 (38108) hydrogen bonds : bond 0.03154 / 2.15 ( 1247) hydrogen bonds : angle 3.78720 / 2.70 ( 3500) ********************** 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 249 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.983 Fit side-chains REVERT: A 527 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: A 548 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7842 (tptp) REVERT: A 794 GLU cc_start: 0.8296 (pm20) cc_final: 0.8024 (tp30) REVERT: A 821 ASP cc_start: 0.8230 (t70) cc_final: 0.7892 (t70) REVERT: A 873 ARG cc_start: 0.8244 (mpp80) cc_final: 0.7797 (mpp80) REVERT: A 876 ASP cc_start: 0.8645 (m-30) cc_final: 0.8111 (m-30) REVERT: E 102 TRP cc_start: 0.8250 (m100) cc_final: 0.8016 (m100) REVERT: E 527 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: E 548 LYS cc_start: 0.8423 (ttpt) cc_final: 0.7908 (tptp) REVERT: E 794 GLU cc_start: 0.8306 (pm20) cc_final: 0.8042 (tp30) REVERT: E 873 ARG cc_start: 0.8267 (mpp80) cc_final: 0.7828 (mpp80) REVERT: E 876 ASP cc_start: 0.8635 (m-30) cc_final: 0.8065 (m-30) outliers start: 30 outliers final: 24 residues processed: 240 average time/residue: 0.1751 time to fit residues: 69.0488 Evaluate side-chains 215 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 1314 ASP Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 497 THR Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 1356 VAL Chi-restraints excluded: chain E residue 1400 ILE Chi-restraints excluded: chain E residue 1482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 208 optimal weight: 0.8980 chunk 240 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 162 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106101 restraints weight = 35364.404| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.08 r_work: 0.3152 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27726 Z= 0.093 Angle : 0.441 8.176 38108 Z= 0.233 Chirality : 0.037 0.160 4374 Planarity : 0.003 0.043 4426 Dihedral : 4.889 53.661 4738 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.12 % Allowed : 12.53 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 2972 helix: 1.47 (0.14), residues: 1446 sheet: -0.70 (0.28), residues: 318 loop : 0.11 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 346 TYR 0.015 0.001 TYR E1434 PHE 0.019 0.001 PHE E 844 TRP 0.018 0.001 TRP A 102 HIS 0.002 0.000 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (27726) covalent geometry : angle 0.44122 / 0.23 (38108) hydrogen bonds : bond 0.03285 / 2.24 ( 1247) hydrogen bonds : angle 3.79423 / 2.70 ( 3500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7936.27 seconds wall clock time: 151 minutes 4.14 seconds (9064.14 seconds total)