Starting phenix.real_space_refine on Sun Aug 24 09:24:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e58_27906/08_2025/8e58_27906.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e58_27906/08_2025/8e58_27906.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 { model { file = "/net/cci-nas-00/data/ceres_data/8e58_27906/08_2025/8e58_27906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e58_27906/08_2025/8e58_27906.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e58_27906/08_2025/8e58_27906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e58_27906/08_2025/8e58_27906.map" } resolution = 3.0 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= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians I 2 10.91 5 Ca 2 9.91 5 P 1 5.49 5 S 109 5.16 5 C 11967 2.51 5 N 2983 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18449 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8919 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 1068} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "B" 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: "C" 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: "D" 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: "G" 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: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {' CA': 1, 'BBI': 1, 'WFR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {' CA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.15, per 1000 atoms: 0.33 Number of scatterers: 18449 At special positions: 0 Unit cell: (148.162, 138.136, 159.302, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) I 2 52.95 Ca 2 19.99 S 109 16.00 P 1 15.00 O 3385 8.00 N 2983 7.00 C 11967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.03 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.03 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 1 " - " ASN F 350 " " NAG C 1 " - " ASN F 615 " " NAG D 1 " - " ASN F 898 " " NAG F1203 " - " ASN F 891 " " NAG F1204 " - " ASN F 92 " " NAG F1205 " - " ASN F 606 " " NAG F1206 " - " ASN F 784 " " NAG F1207 " - " ASN F1001 " " NAG F1208 " - " ASN F 988 " " NAG H 1 " - " ASN F 827 " " NAG I 1 " - " ASN F 186 " " NAG J 1 " - " ASN F 470 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 16 sheets defined 56.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 53 through 70 removed outlier: 3.558A pdb=" N ILE A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 108 removed outlier: 4.129A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 143 removed outlier: 3.649A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.527A pdb=" N LEU A 164 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 168 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 removed outlier: 4.045A pdb=" N LEU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 196 through 218 Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.506A pdb=" N VAL A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 Processing helix chain 'A' and resid 322 through 346 removed outlier: 4.236A pdb=" N SER A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 450 Processing helix chain 'A' and resid 457 through 486 removed outlier: 3.886A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.965A pdb=" N PHE A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 520 through 530 removed outlier: 3.850A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 530 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 534 removed outlier: 3.748A pdb=" N ARG A 534 " --> pdb=" O ARG A 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 531 through 534' Processing helix chain 'A' and resid 535 through 541 removed outlier: 4.467A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.876A pdb=" N SER A 551 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 582 Processing helix chain 'A' and resid 599 through 613 Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.879A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 637 through 672 removed outlier: 4.000A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 818 Processing helix chain 'A' and resid 826 through 851 removed outlier: 3.887A pdb=" N LEU A 849 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.825A pdb=" N SER A 882 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 905 removed outlier: 3.924A pdb=" N VAL A 901 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 902 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 903 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Proline residue: A 904 - end of helix No H-bonds generated for 'chain 'A' and resid 898 through 905' Processing helix chain 'A' and resid 906 through 911 removed outlier: 3.931A pdb=" N ARG A 910 " --> pdb=" O ARG A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 928 Processing helix chain 'A' and resid 929 through 951 Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1015 through 1025 removed outlier: 3.527A pdb=" N LEU A1019 " --> pdb=" O GLY A1015 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A1025 " --> pdb=" O TYR A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1040 No H-bonds generated for 'chain 'A' and resid 1038 through 1040' Processing helix chain 'A' and resid 1041 through 1052 removed outlier: 3.937A pdb=" N PHE A1045 " --> pdb=" O MET A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1072 removed outlier: 3.541A pdb=" N VAL A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A1071 " --> pdb=" O THR A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1095 Processing helix chain 'A' and resid 1105 through 1117 removed outlier: 3.923A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1137 removed outlier: 3.518A pdb=" N MET A1137 " --> pdb=" O ILE A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1173 removed outlier: 3.586A pdb=" N LEU A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1206 Processing helix chain 'A' and resid 1233 through 1238 removed outlier: 3.650A pdb=" N ARG A1236 " --> pdb=" O ALA A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1249 removed outlier: 3.534A pdb=" N LEU A1243 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A1245 " --> pdb=" O ARG A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1267 removed outlier: 3.605A pdb=" N PHE A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1267 " --> pdb=" O SER A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1290 removed outlier: 4.174A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A1275 " --> pdb=" O ALA A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1321 Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1356 through 1383 Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1395 through 1409 removed outlier: 3.841A pdb=" N LEU A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1429 removed outlier: 3.539A pdb=" N VAL A1422 " --> pdb=" O LYS A1418 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A1423 " --> pdb=" O HIS A1419 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 27 removed outlier: 4.008A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 130 removed outlier: 3.610A pdb=" N PHE E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 134 through 135 No H-bonds generated for 'chain 'E' and resid 134 through 135' Processing helix chain 'E' and resid 136 through 165 removed outlier: 3.673A pdb=" N ALA E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 204 Processing helix chain 'F' and resid 29 through 53 Processing helix chain 'F' and resid 53 through 65 removed outlier: 3.831A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN F 65 " --> pdb=" O TYR F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 110 removed outlier: 4.000A pdb=" N VAL F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 removed outlier: 4.498A pdb=" N ASN F 138 " --> pdb=" O PRO F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 Processing helix chain 'F' and resid 190 through 202 removed outlier: 4.437A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 242 Processing helix chain 'F' and resid 243 through 251 removed outlier: 3.802A pdb=" N ALA F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 283 removed outlier: 3.579A pdb=" N LYS F 272 " --> pdb=" O GLY F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 334 through 347 removed outlier: 3.535A pdb=" N GLY F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 removed outlier: 3.549A pdb=" N PHE F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 406 Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'F' and resid 420 through 425 Processing helix chain 'F' and resid 428 through 433 Processing helix chain 'F' and resid 433 through 440 removed outlier: 3.949A pdb=" N GLY F 440 " --> pdb=" O MET F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 444 removed outlier: 3.575A pdb=" N LYS F 444 " --> pdb=" O ASP F 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 441 through 444' Processing helix chain 'F' and resid 481 through 484 removed outlier: 3.798A pdb=" N GLN F 484 " --> pdb=" O LEU F 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 481 through 484' Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 542 through 546 removed outlier: 3.964A pdb=" N ARG F 546 " --> pdb=" O LEU F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 582 removed outlier: 3.904A pdb=" N GLU F 575 " --> pdb=" O ASP F 571 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 582 " --> pdb=" O ASN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 651 removed outlier: 3.746A pdb=" N LEU F 651 " --> pdb=" O TYR F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 654 No H-bonds generated for 'chain 'F' and resid 652 through 654' Processing helix chain 'F' and resid 655 through 660 Processing helix chain 'F' and resid 678 through 693 removed outlier: 3.754A pdb=" N LYS F 693 " --> pdb=" O PHE F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 722 Processing helix chain 'F' and resid 748 through 755 removed outlier: 4.547A pdb=" N GLU F 753 " --> pdb=" O GLU F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 763 Processing helix chain 'F' and resid 764 through 773 Processing helix chain 'F' and resid 820 through 830 Processing helix chain 'F' and resid 877 through 881 Processing helix chain 'F' and resid 882 through 892 Processing helix chain 'F' and resid 1045 through 1050 removed outlier: 3.647A pdb=" N MET F1049 " --> pdb=" O ASP F1045 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL F1050 " --> pdb=" O PRO F1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1045 through 1050' Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 955 through 957 Processing sheet with id=AA3, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA4, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=AA6, first strand: chain 'F' and resid 124 through 125 removed outlier: 5.934A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.709A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER F 495 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU F 460 " --> pdb=" O SER F 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.709A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER F 495 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU F 460 " --> pdb=" O SER F 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'F' and resid 300 through 302 removed outlier: 6.302A pdb=" N LYS F 254 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ASN F 292 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET F 256 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N TYR F 413 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR F 388 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE F 415 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER F 390 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 523 through 525 removed outlier: 6.308A pdb=" N ALA F 516 " --> pdb=" O LEU F 524 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR F 592 " --> pdb=" O GLY F 605 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 540 through 541 Processing sheet with id=AB4, first strand: chain 'F' and resid 661 through 664 removed outlier: 3.896A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS F 818 " --> pdb=" O LYS F 733 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ARG F 735 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY F 816 " --> pdb=" O ARG F 735 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL F 737 " --> pdb=" O VAL F 814 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL F 814 " --> pdb=" O VAL F 737 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 803 through 804 Processing sheet with id=AB6, first strand: chain 'F' and resid 862 through 864 removed outlier: 6.546A pdb=" N ILE F 855 " --> pdb=" O LEU F 863 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET F1020 " --> pdb=" O HIS F1007 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU F1022 " --> pdb=" O ILE F1005 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 896 through 907 removed outlier: 4.911A pdb=" N PHE F 897 " --> pdb=" O PHE F 985 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE F 985 " --> pdb=" O PHE F 897 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS F 899 " --> pdb=" O GLN F 983 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLN F 983 " --> pdb=" O LYS F 899 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TYR F 901 " --> pdb=" O GLN F 981 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN F 981 " --> pdb=" O TYR F 901 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR F 903 " --> pdb=" O THR F 979 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR F 979 " --> pdb=" O TYR F 903 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER F 905 " --> pdb=" O CYS F 977 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) 959 hydrogen bonds defined for protein. 2738 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: 3.97 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 5859 1.37 - 1.52: 8874 1.52 - 1.68: 3965 1.68 - 1.83: 171 1.83 - 1.99: 2 Bond restraints: 18871 Sorted by residual: bond pdb=" O18 WFR A1903 " pdb=" P19 WFR A1903 " ideal model delta sigma weight residual 1.592 1.793 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C02 WFR A1903 " pdb=" C03 WFR A1903 " ideal model delta sigma weight residual 1.520 1.673 -0.153 2.00e-02 2.50e+03 5.89e+01 bond pdb=" O20 WFR A1903 " pdb=" P19 WFR A1903 " ideal model delta sigma weight residual 1.610 1.757 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C31 WFR A1903 " pdb=" C36 WFR A1903 " ideal model delta sigma weight residual 1.388 1.521 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C04 WFR A1903 " pdb=" C09 WFR A1903 " ideal model delta sigma weight residual 1.461 1.585 -0.124 2.00e-02 2.50e+03 3.86e+01 ... (remaining 18866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 25334 2.72 - 5.44: 226 5.44 - 8.17: 29 8.17 - 10.89: 14 10.89 - 13.61: 2 Bond angle restraints: 25605 Sorted by residual: angle pdb=" C LYS F 674 " pdb=" N PRO F 675 " pdb=" CA PRO F 675 " ideal model delta sigma weight residual 119.78 114.61 5.17 1.03e+00 9.43e-01 2.52e+01 angle pdb=" CB LYS A 894 " pdb=" CG LYS A 894 " pdb=" CD LYS A 894 " ideal model delta sigma weight residual 111.30 121.78 -10.48 2.30e+00 1.89e-01 2.08e+01 angle pdb=" CAM BBI A1902 " pdb=" CAN BBI A1902 " pdb=" CAP BBI A1902 " ideal model delta sigma weight residual 118.51 132.12 -13.61 3.00e+00 1.11e-01 2.06e+01 angle pdb=" CA LYS E 132 " pdb=" CB LYS E 132 " pdb=" CG LYS E 132 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CAC BBI A1902 " pdb=" CAD BBI A1902 " pdb=" CAE BBI A1902 " ideal model delta sigma weight residual 112.57 123.85 -11.28 3.00e+00 1.11e-01 1.41e+01 ... (remaining 25600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.40: 10431 21.40 - 42.80: 905 42.80 - 64.20: 156 64.20 - 85.60: 34 85.60 - 106.99: 17 Dihedral angle restraints: 11543 sinusoidal: 4956 harmonic: 6587 Sorted by residual: dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual -86.00 -146.88 60.88 1 1.00e+01 1.00e-02 4.93e+01 dihedral pdb=" CB CYS A 226 " pdb=" SG CYS A 226 " pdb=" SG CYS A 254 " pdb=" CB CYS A 254 " ideal model delta sinusoidal sigma weight residual 93.00 46.53 46.47 1 1.00e+01 1.00e-02 2.99e+01 dihedral pdb=" CA CYS F 406 " pdb=" C CYS F 406 " pdb=" N GLU F 407 " pdb=" CA GLU F 407 " ideal model delta harmonic sigma weight residual 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 11540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 2934 0.190 - 0.380: 12 0.380 - 0.570: 3 0.570 - 0.759: 2 0.759 - 0.949: 1 Chirality restraints: 2952 Sorted by residual: chirality pdb=" P19 WFR A1903 " pdb=" O18 WFR A1903 " pdb=" O20 WFR A1903 " pdb=" O21 WFR A1903 " both_signs ideal model delta sigma weight residual True 2.75 -3.70 -0.95 2.00e-01 2.50e+01 2.25e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN F 350 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C23 WFR A1903 " pdb=" C24 WFR A1903 " pdb=" C25 WFR A1903 " pdb=" N22 WFR A1903 " both_signs ideal model delta sigma weight residual False 2.23 2.85 -0.62 2.00e-01 2.50e+01 9.49e+00 ... (remaining 2949 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 132 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C LYS E 132 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS E 132 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG E 133 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 51 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 52 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 846 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" CD GLU A 846 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 846 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 846 " -0.011 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.75: 2728 2.75 - 3.30: 18504 3.30 - 3.86: 31256 3.86 - 4.41: 38266 4.41 - 4.96: 64627 Nonbonded interactions: 155381 Sorted by model distance: nonbonded pdb=" OG1 THR F 694 " pdb=" OD1 ASN F 696 " model vdw 2.199 3.040 nonbonded pdb=" O LEU A 849 " pdb=" OG1 THR A 852 " model vdw 2.228 3.040 nonbonded pdb=" O ALA A 838 " pdb=" OG SER A 841 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR A1259 " pdb=" OD1 ASN A1383 " model vdw 2.240 3.040 nonbonded pdb=" OG SER F 596 " pdb=" O ASP F 598 " model vdw 2.242 3.040 ... (remaining 155376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) } 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=0.00 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.310 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.007 0.201 18906 Z= 0.307 Angle : 0.744 20.000 25697 Z= 0.350 Chirality : 0.055 0.949 2952 Planarity : 0.004 0.049 3192 Dihedral : 16.489 106.995 7250 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.48 % Rotamer: Outliers : 0.91 % Allowed : 13.05 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 0.19 (0.18), residues: 2212 helix: 1.40 (0.15), residues: 1107 sheet: 0.20 (0.36), residues: 210 loop : -1.57 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 199 TYR 0.014 0.002 TYR F 514 PHE 0.018 0.002 PHE E 152 TRP 0.010 0.001 TRP A 990 HIS 0.008 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00668 (18871) covalent geometry : angle 0.70357 (25605) SS BOND : bond 0.00281 ( 13) SS BOND : angle 1.48743 ( 26) hydrogen bonds : bond 0.16185 ( 946) hydrogen bonds : angle 5.73683 ( 2738) link_BETA1-4 : bond 0.00488 ( 10) link_BETA1-4 : angle 2.30152 ( 30) link_NAG-ASN : bond 0.01403 ( 12) link_NAG-ASN : angle 6.07000 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 500 ASP cc_start: 0.7300 (t0) cc_final: 0.7009 (t0) REVERT: A 983 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8214 (mtt) REVERT: E 53 LEU cc_start: 0.6994 (mm) cc_final: 0.6466 (mp) REVERT: F 569 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7483 (tm-30) REVERT: F 723 TRP cc_start: 0.8542 (m-10) cc_final: 0.8223 (m-10) outliers start: 18 outliers final: 7 residues processed: 241 average time/residue: 0.5124 time to fit residues: 143.3805 Evaluate side-chains 228 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 988 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN E 209 GLN F 108 GLN F 679 ASN F 822 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111578 restraints weight = 36567.335| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.80 r_work: 0.3033 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18906 Z= 0.156 Angle : 0.632 20.448 25697 Z= 0.309 Chirality : 0.045 0.435 2952 Planarity : 0.004 0.052 3192 Dihedral : 8.423 64.168 3015 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.32 % Allowed : 12.55 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 0.41 (0.18), residues: 2212 helix: 1.63 (0.15), residues: 1117 sheet: 0.11 (0.36), residues: 210 loop : -1.50 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 199 TYR 0.014 0.001 TYR A1360 PHE 0.014 0.001 PHE A1060 TRP 0.009 0.001 TRP A 990 HIS 0.006 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00358 (18871) covalent geometry : angle 0.58582 (25605) SS BOND : bond 0.00293 ( 13) SS BOND : angle 1.23981 ( 26) hydrogen bonds : bond 0.04838 ( 946) hydrogen bonds : angle 4.47599 ( 2738) link_BETA1-4 : bond 0.00433 ( 10) link_BETA1-4 : angle 2.04655 ( 30) link_NAG-ASN : bond 0.01178 ( 12) link_NAG-ASN : angle 6.02463 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 0.724 Fit side-chains REVERT: A 224 LYS cc_start: 0.8743 (mttp) cc_final: 0.8478 (mtpp) REVERT: A 666 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7283 (tp30) REVERT: A 894 LYS cc_start: 0.6367 (mmmt) cc_final: 0.5091 (mttp) REVERT: A 983 MET cc_start: 0.8938 (mtp) cc_final: 0.8637 (mtm) REVERT: E 53 LEU cc_start: 0.7154 (mm) cc_final: 0.6754 (mp) REVERT: E 127 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8104 (mtt) REVERT: E 165 MET cc_start: 0.4035 (OUTLIER) cc_final: 0.3140 (tpt) REVERT: F 108 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.9056 (tm-30) REVERT: F 199 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6834 (tmm-80) REVERT: F 497 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8307 (mm-30) REVERT: F 546 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.6992 (tpt170) REVERT: F 569 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7891 (tm-30) REVERT: F 603 ASP cc_start: 0.8739 (m-30) cc_final: 0.8228 (m-30) REVERT: F 997 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7280 (tp) outliers start: 46 outliers final: 13 residues processed: 269 average time/residue: 0.5372 time to fit residues: 166.2891 Evaluate side-chains 252 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 997 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 74 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 52 optimal weight: 0.0270 chunk 217 optimal weight: 8.9990 chunk 145 optimal weight: 0.3980 chunk 177 optimal weight: 0.7980 chunk 206 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN F 424 ASN F 679 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.160176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115276 restraints weight = 32822.614| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.75 r_work: 0.3070 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18906 Z= 0.110 Angle : 0.582 19.719 25697 Z= 0.281 Chirality : 0.043 0.409 2952 Planarity : 0.004 0.050 3192 Dihedral : 6.910 54.276 2999 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.37 % Allowed : 13.56 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 0.68 (0.18), residues: 2212 helix: 1.84 (0.16), residues: 1117 sheet: 0.23 (0.36), residues: 208 loop : -1.35 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 199 TYR 0.011 0.001 TYR A1360 PHE 0.020 0.001 PHE A1125 TRP 0.013 0.001 TRP F 187 HIS 0.002 0.001 HIS F 888 Details of bonding type rmsd covalent geometry : bond 0.00229 (18871) covalent geometry : angle 0.53473 (25605) SS BOND : bond 0.00217 ( 13) SS BOND : angle 0.93939 ( 26) hydrogen bonds : bond 0.03942 ( 946) hydrogen bonds : angle 4.23391 ( 2738) link_BETA1-4 : bond 0.00455 ( 10) link_BETA1-4 : angle 2.02767 ( 30) link_NAG-ASN : bond 0.01202 ( 12) link_NAG-ASN : angle 5.83148 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 224 LYS cc_start: 0.8679 (mttp) cc_final: 0.8458 (mtpp) REVERT: A 260 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7717 (pp20) REVERT: A 482 LYS cc_start: 0.5069 (mmmt) cc_final: 0.4383 (mttt) REVERT: A 654 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7451 (t0) REVERT: A 666 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: A 894 LYS cc_start: 0.6184 (mmmt) cc_final: 0.5130 (mttp) REVERT: A 1243 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8123 (pt) REVERT: E 53 LEU cc_start: 0.7234 (mm) cc_final: 0.6858 (mp) REVERT: E 165 MET cc_start: 0.4019 (OUTLIER) cc_final: 0.3276 (tpt) REVERT: F 102 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8066 (mp) REVERT: F 184 GLU cc_start: 0.8648 (tp30) cc_final: 0.8434 (tp30) REVERT: F 199 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6868 (tmm-80) REVERT: F 546 ARG cc_start: 0.7697 (tpp-160) cc_final: 0.6829 (tpt170) REVERT: F 594 VAL cc_start: 0.9194 (t) cc_final: 0.8916 (m) REVERT: F 603 ASP cc_start: 0.8675 (m-30) cc_final: 0.8146 (m-30) REVERT: F 997 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7295 (tp) outliers start: 47 outliers final: 17 residues processed: 272 average time/residue: 0.5257 time to fit residues: 165.0331 Evaluate side-chains 253 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 997 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 153 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 138 optimal weight: 0.0370 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN E 209 GLN F 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.161001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115311 restraints weight = 33686.173| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.63 r_work: 0.3085 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18906 Z= 0.106 Angle : 0.572 19.452 25697 Z= 0.276 Chirality : 0.043 0.397 2952 Planarity : 0.004 0.048 3192 Dihedral : 6.234 56.975 2999 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.52 % Allowed : 15.02 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 0.85 (0.18), residues: 2212 helix: 1.97 (0.16), residues: 1117 sheet: 0.29 (0.37), residues: 200 loop : -1.25 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 199 TYR 0.013 0.001 TYR F 804 PHE 0.023 0.001 PHE A1125 TRP 0.013 0.001 TRP F 187 HIS 0.002 0.000 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00224 (18871) covalent geometry : angle 0.52554 (25605) SS BOND : bond 0.00189 ( 13) SS BOND : angle 0.86590 ( 26) hydrogen bonds : bond 0.03581 ( 946) hydrogen bonds : angle 4.11194 ( 2738) link_BETA1-4 : bond 0.00465 ( 10) link_BETA1-4 : angle 1.90605 ( 30) link_NAG-ASN : bond 0.01166 ( 12) link_NAG-ASN : angle 5.79816 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 224 LYS cc_start: 0.8653 (mttp) cc_final: 0.8443 (mtpp) REVERT: A 260 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7716 (pp20) REVERT: A 666 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: A 894 LYS cc_start: 0.6134 (mmmt) cc_final: 0.5176 (mttp) REVERT: A 1243 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8024 (pt) REVERT: E 53 LEU cc_start: 0.7171 (mm) cc_final: 0.6844 (mp) REVERT: E 142 MET cc_start: 0.8296 (mpp) cc_final: 0.8081 (mmm) REVERT: E 165 MET cc_start: 0.4203 (OUTLIER) cc_final: 0.3077 (tpt) REVERT: F 102 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7987 (mp) REVERT: F 108 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8945 (tm-30) REVERT: F 283 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7872 (tm-30) REVERT: F 546 ARG cc_start: 0.7679 (tpp-160) cc_final: 0.6856 (tpt170) REVERT: F 584 GLU cc_start: 0.7812 (tt0) cc_final: 0.7542 (mt-10) REVERT: F 594 VAL cc_start: 0.9192 (t) cc_final: 0.8931 (m) REVERT: F 603 ASP cc_start: 0.8649 (m-30) cc_final: 0.8129 (m-30) REVERT: F 997 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7267 (tp) outliers start: 50 outliers final: 15 residues processed: 276 average time/residue: 0.5172 time to fit residues: 165.4158 Evaluate side-chains 255 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 997 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 3 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 202 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 154 optimal weight: 0.1980 chunk 156 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115275 restraints weight = 36060.545| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.97 r_work: 0.3069 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 18906 Z= 0.111 Angle : 0.575 19.428 25697 Z= 0.277 Chirality : 0.043 0.393 2952 Planarity : 0.004 0.046 3192 Dihedral : 6.064 57.045 2999 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.47 % Allowed : 16.18 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 0.90 (0.18), residues: 2212 helix: 2.00 (0.16), residues: 1118 sheet: 0.31 (0.37), residues: 200 loop : -1.21 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 199 TYR 0.011 0.001 TYR A1360 PHE 0.025 0.001 PHE A1125 TRP 0.011 0.001 TRP A 309 HIS 0.003 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00246 (18871) covalent geometry : angle 0.53003 (25605) SS BOND : bond 0.00192 ( 13) SS BOND : angle 0.89099 ( 26) hydrogen bonds : bond 0.03537 ( 946) hydrogen bonds : angle 4.08245 ( 2738) link_BETA1-4 : bond 0.00433 ( 10) link_BETA1-4 : angle 1.83649 ( 30) link_NAG-ASN : bond 0.01162 ( 12) link_NAG-ASN : angle 5.75427 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 224 LYS cc_start: 0.8466 (mttp) cc_final: 0.8252 (mtpp) REVERT: A 260 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7482 (pp20) REVERT: A 654 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7320 (t0) REVERT: A 666 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7150 (tp30) REVERT: A 894 LYS cc_start: 0.6108 (mmmt) cc_final: 0.5155 (mttp) REVERT: A 1243 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7957 (pt) REVERT: E 53 LEU cc_start: 0.7188 (mm) cc_final: 0.6887 (mp) REVERT: E 165 MET cc_start: 0.4455 (OUTLIER) cc_final: 0.3119 (tpt) REVERT: F 283 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7767 (tm-30) REVERT: F 546 ARG cc_start: 0.7538 (tpp-160) cc_final: 0.6742 (tpt170) REVERT: F 594 VAL cc_start: 0.9128 (t) cc_final: 0.8852 (m) REVERT: F 603 ASP cc_start: 0.8444 (m-30) cc_final: 0.7910 (m-30) REVERT: F 892 ILE cc_start: 0.8148 (tp) cc_final: 0.7918 (pt) REVERT: F 997 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7151 (tp) outliers start: 49 outliers final: 23 residues processed: 271 average time/residue: 0.4923 time to fit residues: 155.7042 Evaluate side-chains 261 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 869 ASP Chi-restraints excluded: chain F residue 997 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 64 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 181 optimal weight: 0.0050 chunk 205 optimal weight: 0.9990 chunk 105 optimal weight: 0.0170 chunk 149 optimal weight: 0.1980 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN F 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115284 restraints weight = 31857.267| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.47 r_work: 0.3121 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18906 Z= 0.104 Angle : 0.571 19.380 25697 Z= 0.274 Chirality : 0.042 0.385 2952 Planarity : 0.004 0.046 3192 Dihedral : 5.887 58.481 2999 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.42 % Allowed : 16.68 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 0.98 (0.18), residues: 2212 helix: 2.08 (0.16), residues: 1117 sheet: 0.33 (0.37), residues: 200 loop : -1.18 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 199 TYR 0.011 0.001 TYR A 834 PHE 0.031 0.001 PHE F1006 TRP 0.013 0.001 TRP F 187 HIS 0.004 0.000 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00220 (18871) covalent geometry : angle 0.52640 (25605) SS BOND : bond 0.00178 ( 13) SS BOND : angle 0.78390 ( 26) hydrogen bonds : bond 0.03372 ( 946) hydrogen bonds : angle 4.02356 ( 2738) link_BETA1-4 : bond 0.00433 ( 10) link_BETA1-4 : angle 1.75438 ( 30) link_NAG-ASN : bond 0.01163 ( 12) link_NAG-ASN : angle 5.71209 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.7520 (mtm) cc_final: 0.7240 (mtp) REVERT: A 654 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7374 (t0) REVERT: A 666 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7175 (tp30) REVERT: A 894 LYS cc_start: 0.6008 (mmmt) cc_final: 0.5063 (mttp) REVERT: A 1243 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7870 (pt) REVERT: E 53 LEU cc_start: 0.7244 (mm) cc_final: 0.6965 (mp) REVERT: E 165 MET cc_start: 0.4661 (OUTLIER) cc_final: 0.3181 (tpt) REVERT: F 108 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8884 (tm-30) REVERT: F 283 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7815 (tm-30) REVERT: F 497 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8417 (mm-30) REVERT: F 546 ARG cc_start: 0.7663 (tpp-160) cc_final: 0.6830 (tpt170) REVERT: F 594 VAL cc_start: 0.9173 (t) cc_final: 0.8919 (m) REVERT: F 603 ASP cc_start: 0.8635 (m-30) cc_final: 0.8099 (m-30) REVERT: F 882 ASP cc_start: 0.8543 (t0) cc_final: 0.8189 (t0) outliers start: 48 outliers final: 20 residues processed: 269 average time/residue: 0.4169 time to fit residues: 131.0287 Evaluate side-chains 261 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 749 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 154 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 chunk 198 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN E 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113510 restraints weight = 35479.273| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.71 r_work: 0.3069 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18906 Z= 0.129 Angle : 0.588 19.454 25697 Z= 0.284 Chirality : 0.044 0.389 2952 Planarity : 0.004 0.045 3192 Dihedral : 5.897 59.113 2999 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.32 % Allowed : 17.19 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 0.92 (0.18), residues: 2212 helix: 2.03 (0.16), residues: 1117 sheet: 0.32 (0.37), residues: 200 loop : -1.21 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 199 TYR 0.014 0.001 TYR A 834 PHE 0.029 0.001 PHE A1125 TRP 0.011 0.001 TRP F 187 HIS 0.004 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00300 (18871) covalent geometry : angle 0.54514 (25605) SS BOND : bond 0.00200 ( 13) SS BOND : angle 0.97863 ( 26) hydrogen bonds : bond 0.03598 ( 946) hydrogen bonds : angle 4.04511 ( 2738) link_BETA1-4 : bond 0.00426 ( 10) link_BETA1-4 : angle 1.74044 ( 30) link_NAG-ASN : bond 0.01106 ( 12) link_NAG-ASN : angle 5.69539 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7581 (mtm) cc_final: 0.7305 (mtp) REVERT: A 224 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8447 (mtpp) REVERT: A 654 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7433 (t0) REVERT: A 666 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: A 894 LYS cc_start: 0.6035 (mmmt) cc_final: 0.5099 (mttp) REVERT: A 1083 LYS cc_start: 0.4777 (mmtt) cc_final: 0.4532 (mmmt) REVERT: A 1243 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8037 (pt) REVERT: E 53 LEU cc_start: 0.7194 (mm) cc_final: 0.6927 (mp) REVERT: E 165 MET cc_start: 0.4483 (OUTLIER) cc_final: 0.2926 (tpt) REVERT: F 283 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7920 (tm-30) REVERT: F 546 ARG cc_start: 0.7702 (tpp-160) cc_final: 0.7133 (tpt170) REVERT: F 594 VAL cc_start: 0.9191 (t) cc_final: 0.8914 (m) REVERT: F 603 ASP cc_start: 0.8687 (m-30) cc_final: 0.8171 (m-30) REVERT: F 749 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7216 (tttm) REVERT: F 882 ASP cc_start: 0.8654 (t0) cc_final: 0.8235 (t0) REVERT: F 892 ILE cc_start: 0.8204 (tp) cc_final: 0.7974 (pt) REVERT: F 977 CYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8920 (p) REVERT: F 997 LEU cc_start: 0.7601 (pt) cc_final: 0.7302 (tp) outliers start: 46 outliers final: 27 residues processed: 263 average time/residue: 0.4570 time to fit residues: 140.1403 Evaluate side-chains 269 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1383 ASN Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 749 LYS Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 173 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 151 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN F 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.160229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114059 restraints weight = 43033.616| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.94 r_work: 0.3062 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18906 Z= 0.119 Angle : 0.593 19.369 25697 Z= 0.284 Chirality : 0.043 0.385 2952 Planarity : 0.004 0.046 3192 Dihedral : 5.864 58.909 2999 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.17 % Allowed : 18.15 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 0.93 (0.18), residues: 2212 helix: 2.04 (0.16), residues: 1117 sheet: 0.31 (0.37), residues: 200 loop : -1.21 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 199 TYR 0.018 0.001 TYR A 834 PHE 0.034 0.001 PHE F1006 TRP 0.012 0.001 TRP F 187 HIS 0.003 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00271 (18871) covalent geometry : angle 0.55090 (25605) SS BOND : bond 0.00201 ( 13) SS BOND : angle 0.91277 ( 26) hydrogen bonds : bond 0.03543 ( 946) hydrogen bonds : angle 4.04925 ( 2738) link_BETA1-4 : bond 0.00402 ( 10) link_BETA1-4 : angle 1.71978 ( 30) link_NAG-ASN : bond 0.01126 ( 12) link_NAG-ASN : angle 5.68191 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7517 (mtm) cc_final: 0.7221 (mtp) REVERT: A 224 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8245 (mtpp) REVERT: A 666 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7169 (tp30) REVERT: A 894 LYS cc_start: 0.6014 (mmmt) cc_final: 0.5088 (mttp) REVERT: A 1083 LYS cc_start: 0.4732 (mmtt) cc_final: 0.4508 (mmmt) REVERT: A 1243 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8002 (pt) REVERT: E 53 LEU cc_start: 0.7249 (mm) cc_final: 0.6974 (mp) REVERT: E 165 MET cc_start: 0.4505 (OUTLIER) cc_final: 0.2961 (tpt) REVERT: F 283 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7773 (tm-30) REVERT: F 546 ARG cc_start: 0.7579 (tpp-160) cc_final: 0.7056 (tpt170) REVERT: F 594 VAL cc_start: 0.9128 (t) cc_final: 0.8844 (m) REVERT: F 603 ASP cc_start: 0.8446 (m-30) cc_final: 0.7964 (m-30) REVERT: F 882 ASP cc_start: 0.8542 (t0) cc_final: 0.8104 (t0) REVERT: F 892 ILE cc_start: 0.8073 (tp) cc_final: 0.7842 (pt) REVERT: F 977 CYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8514 (p) REVERT: F 997 LEU cc_start: 0.7444 (pt) cc_final: 0.7203 (tp) outliers start: 43 outliers final: 27 residues processed: 258 average time/residue: 0.4823 time to fit residues: 146.0016 Evaluate side-chains 264 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1383 ASN Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 199 optimal weight: 0.4980 chunk 184 optimal weight: 0.4980 chunk 200 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN E 209 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.160173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114661 restraints weight = 30707.145| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.52 r_work: 0.3071 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18906 Z= 0.119 Angle : 0.593 19.370 25697 Z= 0.284 Chirality : 0.043 0.385 2952 Planarity : 0.004 0.046 3192 Dihedral : 5.874 58.908 2999 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.61 % Allowed : 18.60 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 0.93 (0.18), residues: 2212 helix: 2.04 (0.16), residues: 1117 sheet: 0.31 (0.37), residues: 200 loop : -1.21 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 199 TYR 0.018 0.001 TYR A 834 PHE 0.033 0.001 PHE F1006 TRP 0.012 0.001 TRP F 187 HIS 0.003 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00271 (18871) covalent geometry : angle 0.55050 (25605) SS BOND : bond 0.00201 ( 13) SS BOND : angle 0.91227 ( 26) hydrogen bonds : bond 0.03544 ( 946) hydrogen bonds : angle 4.04922 ( 2738) link_BETA1-4 : bond 0.00418 ( 10) link_BETA1-4 : angle 1.71974 ( 30) link_NAG-ASN : bond 0.01126 ( 12) link_NAG-ASN : angle 5.68197 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7548 (mtm) cc_final: 0.7268 (mtp) REVERT: A 224 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8395 (mtpp) REVERT: A 666 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7217 (tp30) REVERT: A 894 LYS cc_start: 0.5985 (mmmt) cc_final: 0.5055 (mttp) REVERT: A 1083 LYS cc_start: 0.4767 (mmtt) cc_final: 0.4528 (mmmt) REVERT: A 1243 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8016 (pt) REVERT: E 53 LEU cc_start: 0.7250 (mm) cc_final: 0.6985 (mp) REVERT: E 165 MET cc_start: 0.4486 (OUTLIER) cc_final: 0.2934 (tpt) REVERT: F 283 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7837 (tm-30) REVERT: F 546 ARG cc_start: 0.7671 (tpp-160) cc_final: 0.7100 (tpt170) REVERT: F 594 VAL cc_start: 0.9165 (t) cc_final: 0.8880 (m) REVERT: F 603 ASP cc_start: 0.8662 (m-30) cc_final: 0.8165 (m-30) REVERT: F 882 ASP cc_start: 0.8593 (t0) cc_final: 0.8155 (t0) REVERT: F 892 ILE cc_start: 0.8126 (tp) cc_final: 0.7887 (pt) REVERT: F 977 CYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8865 (p) REVERT: F 997 LEU cc_start: 0.7539 (pt) cc_final: 0.7253 (tp) outliers start: 32 outliers final: 27 residues processed: 246 average time/residue: 0.4326 time to fit residues: 124.0326 Evaluate side-chains 264 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1383 ASN Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 142 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN E 209 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.156319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111138 restraints weight = 35360.515| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.85 r_work: 0.3003 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18906 Z= 0.214 Angle : 0.674 19.544 25697 Z= 0.329 Chirality : 0.047 0.402 2952 Planarity : 0.004 0.046 3192 Dihedral : 6.243 58.080 2999 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.86 % Allowed : 18.35 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 0.59 (0.18), residues: 2212 helix: 1.80 (0.15), residues: 1117 sheet: 0.18 (0.36), residues: 200 loop : -1.44 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 199 TYR 0.018 0.002 TYR A1360 PHE 0.032 0.002 PHE A1125 TRP 0.008 0.001 TRP E 32 HIS 0.008 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00520 (18871) covalent geometry : angle 0.63571 (25605) SS BOND : bond 0.00286 ( 13) SS BOND : angle 1.41057 ( 26) hydrogen bonds : bond 0.04409 ( 946) hydrogen bonds : angle 4.25224 ( 2738) link_BETA1-4 : bond 0.00486 ( 10) link_BETA1-4 : angle 1.87554 ( 30) link_NAG-ASN : bond 0.01057 ( 12) link_NAG-ASN : angle 5.73394 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.551 Fit side-chains REVERT: A 224 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8424 (mtpp) REVERT: A 241 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8678 (mtmt) REVERT: A 493 MET cc_start: 0.6593 (ptt) cc_final: 0.5453 (mtt) REVERT: A 666 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: A 894 LYS cc_start: 0.6201 (mmmt) cc_final: 0.5209 (mttp) REVERT: A 1243 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8106 (pt) REVERT: E 53 LEU cc_start: 0.7437 (mm) cc_final: 0.7091 (mm) REVERT: E 165 MET cc_start: 0.4708 (OUTLIER) cc_final: 0.3036 (tpt) REVERT: F 102 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8104 (mp) REVERT: F 283 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7936 (tm-30) REVERT: F 546 ARG cc_start: 0.7783 (tpp-160) cc_final: 0.7187 (tpt170) REVERT: F 603 ASP cc_start: 0.8710 (m-30) cc_final: 0.8270 (m-30) REVERT: F 892 ILE cc_start: 0.8243 (tp) cc_final: 0.8011 (pt) REVERT: F 977 CYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8779 (p) REVERT: F 997 LEU cc_start: 0.7708 (pt) cc_final: 0.7358 (tp) outliers start: 37 outliers final: 20 residues processed: 254 average time/residue: 0.4452 time to fit residues: 130.8289 Evaluate side-chains 254 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 163 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN A1383 ASN E 209 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106641 restraints weight = 35571.988| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.65 r_work: 0.3037 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18906 Z= 0.131 Angle : 0.625 18.833 25697 Z= 0.301 Chirality : 0.044 0.398 2952 Planarity : 0.004 0.046 3192 Dihedral : 6.060 56.565 2999 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.46 % Allowed : 19.15 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: 0.71 (0.18), residues: 2212 helix: 1.92 (0.16), residues: 1117 sheet: 0.21 (0.36), residues: 200 loop : -1.41 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 199 TYR 0.014 0.001 TYR A1360 PHE 0.032 0.001 PHE F1006 TRP 0.020 0.001 TRP A 800 HIS 0.004 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00299 (18871) covalent geometry : angle 0.58531 (25605) SS BOND : bond 0.00240 ( 13) SS BOND : angle 1.05356 ( 26) hydrogen bonds : bond 0.03839 ( 946) hydrogen bonds : angle 4.13515 ( 2738) link_BETA1-4 : bond 0.00452 ( 10) link_BETA1-4 : angle 1.75630 ( 30) link_NAG-ASN : bond 0.01148 ( 12) link_NAG-ASN : angle 5.66522 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7494.20 seconds wall clock time: 128 minutes 22.52 seconds (7702.52 seconds total)