Starting phenix.real_space_refine on Sat Dec 9 15:08:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8e_9780/12_2023/6j8e_9780_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8e_9780/12_2023/6j8e_9780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8e_9780/12_2023/6j8e_9780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8e_9780/12_2023/6j8e_9780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8e_9780/12_2023/6j8e_9780_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8e_9780/12_2023/6j8e_9780_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 974 atoms to isotropic. 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 S 94 5.16 5 Na 1 4.78 5 C 6904 2.51 5 N 1646 2.21 5 O 1837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A ARG 922": "NH1" <-> "NH2" Residue "A ARG 937": "NH1" <-> "NH2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A ARG 1312": "NH1" <-> "NH2" Residue "A ARG 1435": "NH1" <-> "NH2" Residue "A ARG 1632": "NH1" <-> "NH2" Residue "A ARG 1638": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10482 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 1004 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 992 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 122, 992 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 998 Chain: "A" Number of atoms: 9193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 9193 Classifications: {'peptide': 1139} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 27, 'TRANS': 1105} Chain breaks: 3 Chain: "D" Number of atoms: 136 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Conformer: "B" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} bond proxies already assigned to first conformer: 115 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' NA': 1, '9Z9': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG D 10 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 10 " occ=0.50 Time building chain proxies: 6.51, per 1000 atoms: 0.62 Number of scatterers: 10482 At special positions: 0 Unit cell: (140.739, 140.739, 109.1, 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 94 16.00 Na 1 11.00 O 1837 8.00 N 1646 7.00 C 6904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=1.84 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS A 910 " distance=2.09 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 918 " distance=2.04 Simple disulfide: pdb=" SG CYS A 950 " - pdb=" SG CYS A 959 " distance=2.05 Simple disulfide: pdb=" SG CYS A1366 " - pdb=" SG CYS A1386 " distance=2.01 Simple disulfide: pdb=" SG CYS A1731 " - pdb=" SG CYS A1746 " distance=2.03 Simple disulfide: pdb=" SG CYS D 1 " - pdb=" SG CYS D 15 " distance=2.03 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 9 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 16 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2106 " - " ASN A1393 " " NAG B 1 " - " ASN A 340 " " NAG E 1 " - " ASN A1382 " " NAG F 1 " - " ASN A1368 " Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 2.1 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 4 sheets defined 60.1% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'A' and resid 118 through 121 No H-bonds generated for 'chain 'A' and resid 118 through 121' Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 129 through 145 removed outlier: 3.658A pdb=" N LEU A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 140 " --> pdb=" O MET A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 174 removed outlier: 3.523A pdb=" N THR A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.934A pdb=" N LEU A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 218 through 221 removed outlier: 3.531A pdb=" N VAL A 221 " --> pdb=" O THR A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.578A pdb=" N ILE A 228 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 269 removed outlier: 3.745A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASP A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.566A pdb=" N ALA A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 411 removed outlier: 3.962A pdb=" N MET A 402 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 403 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 406 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 407 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 409 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 410 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A 411 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 440 removed outlier: 3.540A pdb=" N GLU A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 753 removed outlier: 4.451A pdb=" N LEU A 751 " --> pdb=" O LYS A 747 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 778 removed outlier: 3.525A pdb=" N ILE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 774 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 807 removed outlier: 3.509A pdb=" N ASN A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 805 " --> pdb=" O ILE A 801 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 840 removed outlier: 3.528A pdb=" N LEU A 840 " --> pdb=" O MET A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 removed outlier: 4.254A pdb=" N ARG A 853 " --> pdb=" O ARG A 850 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 855 " --> pdb=" O PHE A 852 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 856 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 857 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 858 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 862 " --> pdb=" O LYS A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 removed outlier: 3.610A pdb=" N MET A 869 " --> pdb=" O PRO A 865 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 878 " --> pdb=" O ILE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 902 removed outlier: 3.623A pdb=" N MET A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 909 removed outlier: 4.121A pdb=" N LYS A 908 " --> pdb=" O GLY A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.574A pdb=" N VAL A 935 " --> pdb=" O SER A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 954 removed outlier: 3.959A pdb=" N ASP A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 953 " --> pdb=" O ASP A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 985 removed outlier: 3.685A pdb=" N VAL A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 971 " --> pdb=" O MET A 967 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1205 removed outlier: 3.587A pdb=" N ARG A1198 " --> pdb=" O TRP A1194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A1199 " --> pdb=" O TRP A1195 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR A1200 " --> pdb=" O ASN A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1227 removed outlier: 3.664A pdb=" N THR A1212 " --> pdb=" O ASN A1208 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A1225 " --> pdb=" O SER A1221 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A1226 " --> pdb=" O SER A1222 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE A1227 " --> pdb=" O GLY A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 3.831A pdb=" N GLU A1233 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A1235 " --> pdb=" O ILE A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1264 removed outlier: 3.944A pdb=" N LYS A1247 " --> pdb=" O GLU A1243 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A1250 " --> pdb=" O ASP A1246 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A1257 " --> pdb=" O PHE A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1271 removed outlier: 3.863A pdb=" N THR A1271 " --> pdb=" O GLN A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1294 removed outlier: 3.530A pdb=" N ILE A1281 " --> pdb=" O LEU A1277 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A1282 " --> pdb=" O ASP A1278 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1288 " --> pdb=" O VAL A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1316 removed outlier: 3.754A pdb=" N ARG A1306 " --> pdb=" O ILE A1302 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR A1307 " --> pdb=" O LYS A1303 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A1308 " --> pdb=" O SER A1304 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG A1309 " --> pdb=" O LEU A1305 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA A1310 " --> pdb=" O ARG A1306 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU A1311 " --> pdb=" O THR A1307 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG A1312 " --> pdb=" O LEU A1308 " (cutoff:3.500A) Proline residue: A1313 - end of helix removed outlier: 5.053A pdb=" N ALA A1316 " --> pdb=" O ARG A1312 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1302 through 1316' Processing helix chain 'A' and resid 1321 through 1358 removed outlier: 3.789A pdb=" N VAL A1326 " --> pdb=" O GLY A1322 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A1333 " --> pdb=" O ALA A1329 " (cutoff:3.500A) Proline residue: A1335 - end of helix removed outlier: 3.738A pdb=" N VAL A1343 " --> pdb=" O ASN A1339 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1391 Processing helix chain 'A' and resid 1409 through 1420 removed outlier: 3.540A pdb=" N LEU A1413 " --> pdb=" O GLY A1409 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A1417 " --> pdb=" O LEU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1432 Processing helix chain 'A' and resid 1447 through 1459 removed outlier: 3.557A pdb=" N TYR A1450 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A1454 " --> pdb=" O LEU A1451 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A1456 " --> pdb=" O PHE A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1482 removed outlier: 3.595A pdb=" N GLN A1478 " --> pdb=" O ASP A1474 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1505 removed outlier: 3.968A pdb=" N LYS A1496 " --> pdb=" O GLU A1492 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR A1498 " --> pdb=" O GLN A1494 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A1500 " --> pdb=" O LYS A1496 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A1501 " --> pdb=" O TYR A1497 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A1503 " --> pdb=" O ASN A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1528 Processing helix chain 'A' and resid 1531 through 1549 removed outlier: 3.840A pdb=" N ILE A1537 " --> pdb=" O PHE A1533 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A1538 " --> pdb=" O ASP A1534 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A1547 " --> pdb=" O LEU A1543 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A1549 " --> pdb=" O MET A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1584 removed outlier: 3.504A pdb=" N ILE A1571 " --> pdb=" O ASN A1567 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A1582 " --> pdb=" O CYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1593 through 1615 removed outlier: 3.571A pdb=" N VAL A1600 " --> pdb=" O ILE A1596 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A1612 " --> pdb=" O GLY A1608 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A1613 " --> pdb=" O MET A1609 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A1614 " --> pdb=" O PHE A1610 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1633 removed outlier: 3.944A pdb=" N VAL A1627 " --> pdb=" O THR A1623 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A1629 " --> pdb=" O PHE A1625 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A1630 " --> pdb=" O ARG A1626 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA A1631 " --> pdb=" O VAL A1627 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ARG A1632 " --> pdb=" O ILE A1628 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE A1633 " --> pdb=" O ARG A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1641 Processing helix chain 'A' and resid 1646 through 1654 Processing helix chain 'A' and resid 1657 through 1681 removed outlier: 3.589A pdb=" N ILE A1663 " --> pdb=" O ALA A1659 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A1666 " --> pdb=" O ASN A1662 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1670 " --> pdb=" O LEU A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1700 through 1711 removed outlier: 3.614A pdb=" N ILE A1705 " --> pdb=" O GLY A1701 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A1709 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1716 through 1721 Processing helix chain 'A' and resid 1749 through 1784 removed outlier: 3.507A pdb=" N MET A1770 " --> pdb=" O VAL A1766 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A1777 " --> pdb=" O ALA A1773 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A1780 " --> pdb=" O LEU A1776 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A1782 " --> pdb=" O ASN A1778 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A1784 " --> pdb=" O SER A1780 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 12 Processing sheet with id= A, first strand: chain 'C' and resid 37 through 41 removed outlier: 7.686A pdb=" N LEU C 38 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS C 143 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL C 40 " --> pdb=" O HIS C 143 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN C 145 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 46 through 48 Processing sheet with id= C, first strand: chain 'A' and resid 276 through 280 Processing sheet with id= D, first strand: chain 'A' and resid 1365 through 1368 476 hydrogen bonds defined for protein. 1339 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 3223 1.36 - 1.52: 5746 1.52 - 1.69: 1626 1.69 - 1.85: 149 1.85 - 2.01: 1 Bond restraints: 10745 Sorted by residual: bond pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " ideal model delta sigma weight residual 1.808 2.011 -0.203 3.30e-02 9.18e+02 3.77e+01 bond pdb=" C ILE A1334 " pdb=" N PRO A1335 " ideal model delta sigma weight residual 1.336 1.407 -0.072 1.23e-02 6.61e+03 3.40e+01 bond pdb=" C GLN C 96 " pdb=" N ASP C 97 " ideal model delta sigma weight residual 1.332 1.245 0.086 1.52e-02 4.33e+03 3.23e+01 bond pdb=" N PRO A 921 " pdb=" CD PRO A 921 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.68e+01 bond pdb=" CA AARG D 10 " pdb=" C AARG D 10 " ideal model delta sigma weight residual 1.524 1.585 -0.061 1.27e-02 6.20e+03 2.32e+01 ... (remaining 10740 not shown) Histogram of bond angle deviations from ideal: 92.82 - 102.79: 83 102.79 - 112.77: 5562 112.77 - 122.74: 8102 122.74 - 132.71: 788 132.71 - 142.68: 38 Bond angle restraints: 14573 Sorted by residual: angle pdb=" CA AARG D 10 " pdb=" C AARG D 10 " pdb=" O AARG D 10 " ideal model delta sigma weight residual 120.82 136.81 -15.99 1.05e+00 9.07e-01 2.32e+02 angle pdb=" O GLN C 96 " pdb=" C GLN C 96 " pdb=" N ASP C 97 " ideal model delta sigma weight residual 122.59 142.68 -20.09 1.33e+00 5.65e-01 2.28e+02 angle pdb=" CA AARG D 10 " pdb=" C AARG D 10 " pdb=" N ASP D 11 " ideal model delta sigma weight residual 117.07 102.57 14.50 1.14e+00 7.69e-01 1.62e+02 angle pdb=" N AARG D 10 " pdb=" CA AARG D 10 " pdb=" C AARG D 10 " ideal model delta sigma weight residual 111.07 124.56 -13.49 1.07e+00 8.73e-01 1.59e+02 angle pdb=" N ASN A 212 " pdb=" CA ASN A 212 " pdb=" CB ASN A 212 " ideal model delta sigma weight residual 110.49 131.53 -21.04 1.69e+00 3.50e-01 1.55e+02 ... (remaining 14568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 6082 22.99 - 45.98: 336 45.98 - 68.97: 55 68.97 - 91.95: 9 91.95 - 114.94: 1 Dihedral angle restraints: 6483 sinusoidal: 2731 harmonic: 3752 Sorted by residual: dihedral pdb=" N ASN A 212 " pdb=" C ASN A 212 " pdb=" CA ASN A 212 " pdb=" CB ASN A 212 " ideal model delta harmonic sigma weight residual 122.80 157.90 -35.10 0 2.50e+00 1.60e-01 1.97e+02 dihedral pdb=" C ASN A 212 " pdb=" N ASN A 212 " pdb=" CA ASN A 212 " pdb=" CB ASN A 212 " ideal model delta harmonic sigma weight residual -122.60 -151.91 29.31 0 2.50e+00 1.60e-01 1.37e+02 dihedral pdb=" CA PRO A1514 " pdb=" C PRO A1514 " pdb=" N ARG A1515 " pdb=" CA ARG A1515 " ideal model delta harmonic sigma weight residual 180.00 135.66 44.34 0 5.00e+00 4.00e-02 7.86e+01 ... (remaining 6480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 1673 0.281 - 0.563: 7 0.563 - 0.844: 2 0.844 - 1.126: 0 1.126 - 1.407: 1 Chirality restraints: 1683 Sorted by residual: chirality pdb=" CA ASN A 212 " pdb=" N ASN A 212 " pdb=" C ASN A 212 " pdb=" CB ASN A 212 " both_signs ideal model delta sigma weight residual False 2.51 1.10 1.41 2.00e-01 2.50e+01 4.95e+01 chirality pdb=" CA TRP A 316 " pdb=" N TRP A 316 " pdb=" C TRP A 316 " pdb=" CB TRP A 316 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.98e+00 chirality pdb=" CA PRO A 744 " pdb=" N PRO A 744 " pdb=" C PRO A 744 " pdb=" CB PRO A 744 " both_signs ideal model delta sigma weight residual False 2.72 2.13 0.58 2.00e-01 2.50e+01 8.55e+00 ... (remaining 1680 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 743 " -0.152 5.00e-02 4.00e+02 2.35e-01 8.82e+01 pdb=" N PRO A 744 " 0.405 5.00e-02 4.00e+02 pdb=" CA PRO A 744 " -0.150 5.00e-02 4.00e+02 pdb=" CD PRO A 744 " -0.104 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA BARG D 10 " 0.033 2.00e-02 2.50e+03 6.79e-02 4.61e+01 pdb=" C BARG D 10 " -0.117 2.00e-02 2.50e+03 pdb=" O BARG D 10 " 0.045 2.00e-02 2.50e+03 pdb=" N ASP D 11 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AARG D 10 " 0.025 2.00e-02 2.50e+03 4.82e-02 2.33e+01 pdb=" C AARG D 10 " -0.083 2.00e-02 2.50e+03 pdb=" O AARG D 10 " 0.035 2.00e-02 2.50e+03 pdb=" N ASP D 11 " 0.023 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 54 2.52 - 3.12: 7258 3.12 - 3.71: 15884 3.71 - 4.31: 22895 4.31 - 4.90: 36741 Nonbonded interactions: 82832 Sorted by model distance: nonbonded pdb=" O THR A1712 " pdb=" OG SER A1713 " model vdw 1.927 2.440 nonbonded pdb=" CG LYS A 743 " pdb=" CD PRO A 744 " model vdw 2.186 3.840 nonbonded pdb=" O LEU A1416 " pdb=" OG1 THR A1420 " model vdw 2.236 2.440 nonbonded pdb=" O LEU A 380 " pdb=" OG SER A 413 " model vdw 2.256 2.440 nonbonded pdb=" CD1 LEU A 436 " pdb=" OE2 GLU A 440 " model vdw 2.299 3.460 ... (remaining 82827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } 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=0.14 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.540 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.940 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 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 : 0.008 0.203 10745 Z= 0.533 Angle : 1.432 30.358 14573 Z= 0.799 Chirality : 0.078 1.407 1683 Planarity : 0.009 0.235 1778 Dihedral : 13.948 114.942 4028 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 1.03 % Allowed : 6.40 % Favored : 92.57 % Rotamer: Outliers : 5.14 % Allowed : 8.71 % Favored : 86.15 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 5.71 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.60 (0.17), residues: 1272 helix: -4.19 (0.09), residues: 774 sheet: -0.78 (0.53), residues: 85 loop : -2.87 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A1348 HIS 0.017 0.002 HIS A 128 PHE 0.047 0.004 PHE A1359 TYR 0.068 0.004 TYR A 907 ARG 0.016 0.002 ARG A1435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 236 time to evaluate : 1.278 Fit side-chains outliers start: 58 outliers final: 12 residues processed: 282 average time/residue: 1.0778 time to fit residues: 331.1622 Evaluate side-chains 155 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.7494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN C 82 GLN C 118 GLN A 132 ASN A 383 GLN A 388 ASN A 418 ASN A 441 GLN A 750 HIS A 868 ASN A 876 ASN A 924 HIS A 971 ASN A1196 ASN A1207 HIS A1272 ASN A1292 ASN A1466 ASN A1595 ASN A1702 ASN A1748 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10745 Z= 0.232 Angle : 0.807 10.265 14573 Z= 0.409 Chirality : 0.043 0.223 1683 Planarity : 0.006 0.096 1778 Dihedral : 7.371 74.128 1617 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.74 % Favored : 94.62 % Rotamer: Outliers : 4.36 % Allowed : 17.33 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.21), residues: 1272 helix: -1.87 (0.16), residues: 763 sheet: -0.72 (0.53), residues: 80 loop : -2.39 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 67 HIS 0.008 0.001 HIS A 750 PHE 0.018 0.002 PHE A 184 TYR 0.019 0.002 TYR A 390 ARG 0.007 0.001 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 167 time to evaluate : 1.161 Fit side-chains outliers start: 49 outliers final: 8 residues processed: 202 average time/residue: 0.8836 time to fit residues: 197.3178 Evaluate side-chains 145 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.7159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 976 ASN A1207 HIS A1778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10745 Z= 0.187 Angle : 0.698 9.545 14573 Z= 0.352 Chirality : 0.041 0.209 1683 Planarity : 0.005 0.080 1778 Dihedral : 6.627 72.066 1617 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.82 % Favored : 94.55 % Rotamer: Outliers : 5.40 % Allowed : 17.60 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.23), residues: 1272 helix: -0.47 (0.18), residues: 763 sheet: -0.53 (0.54), residues: 80 loop : -2.17 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 67 HIS 0.003 0.001 HIS A1207 PHE 0.015 0.001 PHE A 184 TYR 0.018 0.001 TYR A 390 ARG 0.004 0.001 ARG A1638 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 155 time to evaluate : 1.288 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 16 residues processed: 196 average time/residue: 0.8859 time to fit residues: 192.2809 Evaluate side-chains 158 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 0.4754 time to fit residues: 4.9900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN A 268 GLN A1207 HIS A1208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10745 Z= 0.191 Angle : 0.672 9.206 14573 Z= 0.337 Chirality : 0.042 0.211 1683 Planarity : 0.004 0.071 1778 Dihedral : 6.250 70.469 1617 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.14 % Favored : 94.31 % Rotamer: Outliers : 4.62 % Allowed : 18.73 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1272 helix: 0.42 (0.19), residues: 763 sheet: -0.43 (0.53), residues: 80 loop : -2.04 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 864 HIS 0.003 0.001 HIS A1207 PHE 0.012 0.001 PHE C 83 TYR 0.012 0.001 TYR A1759 ARG 0.006 0.000 ARG A1629 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 156 time to evaluate : 1.315 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 20 residues processed: 193 average time/residue: 1.0387 time to fit residues: 222.1221 Evaluate side-chains 162 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 5 average time/residue: 0.8583 time to fit residues: 7.0311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A1725 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10745 Z= 0.285 Angle : 0.692 10.988 14573 Z= 0.349 Chirality : 0.043 0.206 1683 Planarity : 0.005 0.071 1778 Dihedral : 6.313 70.643 1617 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.61 % Favored : 93.83 % Rotamer: Outliers : 5.05 % Allowed : 19.43 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1272 helix: 0.70 (0.19), residues: 770 sheet: -0.37 (0.54), residues: 80 loop : -1.83 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 864 HIS 0.008 0.001 HIS A 750 PHE 0.019 0.002 PHE A 963 TYR 0.026 0.002 TYR A1564 ARG 0.008 0.001 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 150 time to evaluate : 1.145 Fit side-chains outliers start: 57 outliers final: 23 residues processed: 187 average time/residue: 0.9341 time to fit residues: 193.2929 Evaluate side-chains 161 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 8 average time/residue: 0.6822 time to fit residues: 7.8332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10745 Z= 0.273 Angle : 0.694 11.487 14573 Z= 0.347 Chirality : 0.043 0.232 1683 Planarity : 0.004 0.068 1778 Dihedral : 6.255 69.609 1617 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.53 % Favored : 93.91 % Rotamer: Outliers : 4.44 % Allowed : 20.99 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1272 helix: 0.94 (0.19), residues: 764 sheet: -0.48 (0.52), residues: 80 loop : -1.71 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 745 HIS 0.007 0.001 HIS A 750 PHE 0.015 0.001 PHE A 963 TYR 0.018 0.002 TYR A 390 ARG 0.005 0.001 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 19 residues processed: 179 average time/residue: 0.9072 time to fit residues: 180.9410 Evaluate side-chains 157 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 6 average time/residue: 0.6788 time to fit residues: 6.1556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10745 Z= 0.217 Angle : 0.673 10.051 14573 Z= 0.336 Chirality : 0.043 0.318 1683 Planarity : 0.004 0.066 1778 Dihedral : 6.095 68.043 1617 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.45 % Favored : 94.07 % Rotamer: Outliers : 4.18 % Allowed : 21.69 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1272 helix: 1.24 (0.20), residues: 757 sheet: -0.51 (0.52), residues: 80 loop : -1.71 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 745 HIS 0.006 0.001 HIS A 750 PHE 0.013 0.001 PHE A1755 TYR 0.024 0.001 TYR A1564 ARG 0.005 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 149 time to evaluate : 1.299 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 25 residues processed: 182 average time/residue: 0.8419 time to fit residues: 170.8957 Evaluate side-chains 166 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 7 average time/residue: 0.5803 time to fit residues: 6.3560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 30.0000 chunk 95 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10745 Z= 0.237 Angle : 0.692 10.967 14573 Z= 0.344 Chirality : 0.043 0.265 1683 Planarity : 0.004 0.065 1778 Dihedral : 6.060 67.759 1617 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.14 % Favored : 94.39 % Rotamer: Outliers : 3.92 % Allowed : 22.21 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1272 helix: 1.35 (0.20), residues: 758 sheet: -0.51 (0.52), residues: 80 loop : -1.74 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 745 HIS 0.006 0.001 HIS A 750 PHE 0.014 0.001 PHE A 963 TYR 0.016 0.002 TYR A 390 ARG 0.010 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 145 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 24 residues processed: 177 average time/residue: 0.8451 time to fit residues: 167.2144 Evaluate side-chains 165 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 5 average time/residue: 0.5541 time to fit residues: 4.7391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1475 ASN A1769 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10745 Z= 0.230 Angle : 0.684 10.120 14573 Z= 0.339 Chirality : 0.043 0.258 1683 Planarity : 0.004 0.065 1778 Dihedral : 5.984 66.926 1617 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.22 % Favored : 94.31 % Rotamer: Outliers : 3.48 % Allowed : 23.08 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1272 helix: 1.42 (0.20), residues: 765 sheet: -0.12 (0.54), residues: 73 loop : -1.71 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 745 HIS 0.005 0.001 HIS A 750 PHE 0.038 0.001 PHE A1525 TYR 0.024 0.002 TYR A1564 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 173 average time/residue: 0.8411 time to fit residues: 162.7950 Evaluate side-chains 160 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 3 average time/residue: 0.4782 time to fit residues: 3.3899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10745 Z= 0.207 Angle : 0.690 9.619 14573 Z= 0.340 Chirality : 0.042 0.236 1683 Planarity : 0.004 0.064 1778 Dihedral : 5.866 66.077 1617 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.06 % Favored : 94.55 % Rotamer: Outliers : 2.96 % Allowed : 23.78 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1272 helix: 1.52 (0.20), residues: 765 sheet: -0.07 (0.55), residues: 73 loop : -1.72 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 191 HIS 0.005 0.001 HIS A 750 PHE 0.033 0.001 PHE A1525 TYR 0.014 0.001 TYR A 415 ARG 0.005 0.000 ARG A 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 144 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 168 average time/residue: 0.9272 time to fit residues: 173.5027 Evaluate side-chains 168 residues out of total 1139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 7 average time/residue: 0.6112 time to fit residues: 6.5978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.0470 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.135093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089959 restraints weight = 44218.409| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.96 r_work: 0.2973 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10745 Z= 0.175 Angle : 0.678 10.038 14573 Z= 0.332 Chirality : 0.042 0.241 1683 Planarity : 0.004 0.064 1778 Dihedral : 5.647 65.024 1617 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.14 % Favored : 94.47 % Rotamer: Outliers : 2.53 % Allowed : 23.95 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.32 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1272 helix: 1.69 (0.20), residues: 765 sheet: -0.02 (0.55), residues: 73 loop : -1.68 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1424 HIS 0.005 0.001 HIS A 750 PHE 0.030 0.001 PHE A1525 TYR 0.013 0.001 TYR A 415 ARG 0.004 0.000 ARG A 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3821.90 seconds wall clock time: 68 minutes 44.06 seconds (4124.06 seconds total)