Starting phenix.real_space_refine on Mon Jun 16 14:18:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e58_27906/06_2025/8e58_27906.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e58_27906/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e58_27906/06_2025/8e58_27906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e58_27906/06_2025/8e58_27906.map" model { file = "/net/cci-nas-00/data/ceres_data/8e58_27906/06_2025/8e58_27906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e58_27906/06_2025/8e58_27906.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.80, per 1000 atoms: 0.69 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: 4.37 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 1.89 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: 6.42 Time building geometry restraints manager: 5.02 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: 1.440 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 43.030 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.340 ------------------------------------------------------------------------------- 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 : 7.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (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 TRP 0.010 0.001 TRP A 990 HIS 0.008 0.001 HIS A 992 PHE 0.018 0.002 PHE E 152 TYR 0.014 0.002 TYR F 514 ARG 0.008 0.000 ARG F 199 Details of bonding type rmsd link_NAG-ASN : bond 0.01403 ( 12) link_NAG-ASN : angle 6.07000 ( 36) link_BETA1-4 : bond 0.00488 ( 10) link_BETA1-4 : angle 2.30152 ( 30) hydrogen bonds : bond 0.16185 ( 946) hydrogen bonds : angle 5.73683 ( 2738) SS BOND : bond 0.00281 ( 13) SS BOND : angle 1.48743 ( 26) covalent geometry : bond 0.00668 (18871) covalent geometry : angle 0.70357 (25605) *********************** 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 : 2.079 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: 1.1062 time to fit residues: 311.4891 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 : 2.554 ------------------------------------------------------------------------------- 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 188 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A1071 GLN E 209 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 822 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107951 restraints weight = 42673.296| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.04 r_work: 0.2959 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 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 = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18906 Z= 0.246 Angle : 0.692 20.753 25697 Z= 0.344 Chirality : 0.049 0.457 2952 Planarity : 0.005 0.051 3192 Dihedral : 8.796 66.698 3015 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.67 % Allowed : 12.65 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2212 helix: 1.44 (0.15), residues: 1116 sheet: 0.10 (0.35), residues: 213 loop : -1.61 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 990 HIS 0.010 0.001 HIS A 992 PHE 0.019 0.002 PHE F 157 TYR 0.015 0.002 TYR F 514 ARG 0.006 0.001 ARG F 199 Details of bonding type rmsd link_NAG-ASN : bond 0.01151 ( 12) link_NAG-ASN : angle 6.04658 ( 36) link_BETA1-4 : bond 0.00403 ( 10) link_BETA1-4 : angle 2.05117 ( 30) hydrogen bonds : bond 0.05442 ( 946) hydrogen bonds : angle 4.62077 ( 2738) SS BOND : bond 0.00372 ( 13) SS BOND : angle 1.54209 ( 26) covalent geometry : bond 0.00594 (18871) covalent geometry : angle 0.64989 (25605) *********************** 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 290 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 2.005 Fit side-chains REVERT: A 894 LYS cc_start: 0.6518 (mmmt) cc_final: 0.5388 (mppt) REVERT: A 983 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8527 (mtt) REVERT: E 53 LEU cc_start: 0.7185 (mm) cc_final: 0.6760 (mp) REVERT: E 127 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8073 (mtt) REVERT: E 165 MET cc_start: 0.4079 (OUTLIER) cc_final: 0.3177 (tpt) REVERT: F 199 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.6870 (tmm-80) REVERT: F 311 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.7791 (tp40) REVERT: F 497 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8133 (mm-30) REVERT: F 546 ARG cc_start: 0.7759 (tpp-160) cc_final: 0.6898 (tpt170) REVERT: F 569 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7764 (tm-30) REVERT: F 603 ASP cc_start: 0.8557 (m-30) cc_final: 0.8043 (m-30) REVERT: F 858 ASP cc_start: 0.8694 (p0) cc_final: 0.7947 (p0) REVERT: F 864 MET cc_start: 0.7929 (tpp) cc_final: 0.6834 (tpp) outliers start: 53 outliers final: 18 residues processed: 260 average time/residue: 1.2085 time to fit residues: 364.5324 Evaluate side-chains 250 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 2.439 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 525 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 32 optimal weight: 10.0000 chunk 192 optimal weight: 0.0070 chunk 168 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- 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 424 ASN ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1007 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.158728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112555 restraints weight = 35489.724| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.60 r_work: 0.3047 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 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 = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18906 Z= 0.122 Angle : 0.595 19.311 25697 Z= 0.290 Chirality : 0.044 0.422 2952 Planarity : 0.004 0.050 3192 Dihedral : 7.064 53.947 3004 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.27 % Allowed : 14.11 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2212 helix: 1.72 (0.15), residues: 1117 sheet: 0.13 (0.36), residues: 208 loop : -1.47 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 187 HIS 0.003 0.001 HIS F 888 PHE 0.026 0.001 PHE A1125 TYR 0.013 0.001 TYR A1360 ARG 0.006 0.000 ARG F 199 Details of bonding type rmsd link_NAG-ASN : bond 0.01050 ( 12) link_NAG-ASN : angle 5.85055 ( 36) link_BETA1-4 : bond 0.00437 ( 10) link_BETA1-4 : angle 2.05465 ( 30) hydrogen bonds : bond 0.04066 ( 946) hydrogen bonds : angle 4.27140 ( 2738) SS BOND : bond 0.00230 ( 13) SS BOND : angle 1.03216 ( 26) covalent geometry : bond 0.00272 (18871) covalent geometry : angle 0.54920 (25605) *********************** 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 299 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 2.125 Fit side-chains revert: symmetry clash REVERT: A 668 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6606 (pp20) REVERT: A 894 LYS cc_start: 0.6210 (mmmt) cc_final: 0.5135 (mttp) REVERT: A 983 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8704 (mtm) REVERT: A 1243 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8138 (pt) REVERT: E 53 LEU cc_start: 0.7242 (mm) cc_final: 0.6849 (mp) REVERT: E 165 MET cc_start: 0.4247 (OUTLIER) cc_final: 0.2980 (tpt) REVERT: F 102 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8049 (mp) REVERT: F 199 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.6884 (tmm-80) REVERT: F 546 ARG cc_start: 0.7734 (tpp-160) cc_final: 0.6849 (tpt170) REVERT: F 569 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7907 (tm-30) REVERT: F 603 ASP cc_start: 0.8681 (m-30) cc_final: 0.8203 (m-30) REVERT: F 997 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7318 (tp) outliers start: 45 outliers final: 18 residues processed: 276 average time/residue: 1.0205 time to fit residues: 326.6785 Evaluate side-chains 252 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 553 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 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1337 LEU 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 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 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 805 ILE Chi-restraints excluded: chain F residue 869 ASP 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 102 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 115 optimal weight: 30.0000 chunk 3 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108662 restraints weight = 27249.869| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.15 r_work: 0.3096 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1155 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= 0.119 Angle : 0.587 19.509 25697 Z= 0.285 Chirality : 0.044 0.410 2952 Planarity : 0.004 0.049 3192 Dihedral : 6.497 55.878 3002 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.77 % Allowed : 15.17 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2212 helix: 1.83 (0.15), residues: 1117 sheet: 0.20 (0.37), residues: 200 loop : -1.39 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 187 HIS 0.009 0.001 HIS F 867 PHE 0.024 0.001 PHE A1125 TYR 0.011 0.001 TYR A1360 ARG 0.006 0.000 ARG F 199 Details of bonding type rmsd link_NAG-ASN : bond 0.01154 ( 12) link_NAG-ASN : angle 5.80788 ( 36) link_BETA1-4 : bond 0.00416 ( 10) link_BETA1-4 : angle 1.96434 ( 30) hydrogen bonds : bond 0.03834 ( 946) hydrogen bonds : angle 4.19714 ( 2738) SS BOND : bond 0.00226 ( 13) SS BOND : angle 0.98489 ( 26) covalent geometry : bond 0.00262 (18871) covalent geometry : angle 0.54065 (25605) *********************** 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 290 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 235 time to evaluate : 2.142 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7070 (pm20) REVERT: A 493 MET cc_start: 0.6323 (ptt) cc_final: 0.5202 (mtt) REVERT: A 666 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7257 (tp30) REVERT: A 894 LYS cc_start: 0.6278 (mmmt) cc_final: 0.5267 (mttp) REVERT: A 983 MET cc_start: 0.8762 (mtp) cc_final: 0.8543 (mtt) REVERT: A 1243 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8062 (pt) REVERT: E 53 LEU cc_start: 0.7253 (mm) cc_final: 0.6929 (mp) REVERT: E 165 MET cc_start: 0.4102 (OUTLIER) cc_final: 0.3100 (tpt) REVERT: F 546 ARG cc_start: 0.7677 (tpp-160) cc_final: 0.6843 (tpt170) REVERT: F 584 GLU cc_start: 0.7725 (tt0) cc_final: 0.7514 (mt-10) REVERT: F 594 VAL cc_start: 0.9204 (t) cc_final: 0.8903 (m) REVERT: F 603 ASP cc_start: 0.8569 (m-30) cc_final: 0.8077 (m-30) outliers start: 55 outliers final: 24 residues processed: 266 average time/residue: 1.0198 time to fit residues: 317.6576 Evaluate side-chains 251 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 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 509 LEU Chi-restraints excluded: chain A residue 553 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 898 VAL Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1108 GLN 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 1337 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 216 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 994 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 182 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113371 restraints weight = 36003.467| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.72 r_work: 0.3067 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 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 = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18906 Z= 0.113 Angle : 0.577 19.503 25697 Z= 0.279 Chirality : 0.043 0.400 2952 Planarity : 0.004 0.048 3192 Dihedral : 6.160 56.937 2999 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.82 % Allowed : 16.63 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2212 helix: 1.91 (0.16), residues: 1117 sheet: 0.17 (0.37), residues: 200 loop : -1.34 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 187 HIS 0.003 0.001 HIS E 31 PHE 0.026 0.001 PHE A1125 TYR 0.011 0.001 TYR A1360 ARG 0.006 0.000 ARG A 897 Details of bonding type rmsd link_NAG-ASN : bond 0.01149 ( 12) link_NAG-ASN : angle 5.75693 ( 36) link_BETA1-4 : bond 0.00428 ( 10) link_BETA1-4 : angle 1.84629 ( 30) hydrogen bonds : bond 0.03640 ( 946) hydrogen bonds : angle 4.11818 ( 2738) SS BOND : bond 0.00213 ( 13) SS BOND : angle 0.93335 ( 26) covalent geometry : bond 0.00251 (18871) covalent geometry : angle 0.53158 (25605) *********************** 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 299 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 243 time to evaluate : 1.894 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7607 (mtm) cc_final: 0.7392 (mtp) REVERT: A 260 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: A 666 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7275 (tp30) REVERT: A 668 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6607 (pp20) REVERT: A 894 LYS cc_start: 0.6204 (mmmt) cc_final: 0.5178 (mttp) REVERT: A 983 MET cc_start: 0.8804 (mtp) cc_final: 0.8569 (mtt) REVERT: A 1243 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7968 (pt) REVERT: E 53 LEU cc_start: 0.7247 (mm) cc_final: 0.6958 (mp) REVERT: E 127 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8078 (mtt) REVERT: E 142 MET cc_start: 0.8516 (mpp) cc_final: 0.8297 (mmm) REVERT: E 165 MET cc_start: 0.4637 (OUTLIER) cc_final: 0.3169 (tpt) REVERT: F 546 ARG cc_start: 0.7676 (tpp-160) cc_final: 0.6842 (tpt170) REVERT: F 584 GLU cc_start: 0.7830 (tt0) cc_final: 0.7560 (mt-10) REVERT: F 594 VAL cc_start: 0.9197 (t) cc_final: 0.8908 (m) REVERT: F 603 ASP cc_start: 0.8653 (m-30) cc_final: 0.8147 (m-30) REVERT: F 997 LEU cc_start: 0.7633 (pt) cc_final: 0.7381 (tp) outliers start: 56 outliers final: 24 residues processed: 273 average time/residue: 0.9685 time to fit residues: 308.7395 Evaluate side-chains 259 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 477 ILE 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 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 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 1332 CYS Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 151 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 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 591 ARG Chi-restraints excluded: chain F residue 994 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 176 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 168 optimal weight: 0.0970 chunk 158 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 679 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 = 0.3816 r_free = 0.3816 target = 0.157099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113437 restraints weight = 27498.840| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.46 r_work: 0.3072 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 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 = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18906 Z= 0.171 Angle : 0.625 19.701 25697 Z= 0.304 Chirality : 0.045 0.402 2952 Planarity : 0.004 0.046 3192 Dihedral : 6.255 56.345 2999 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.28 % Allowed : 16.83 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2212 helix: 1.80 (0.15), residues: 1117 sheet: 0.12 (0.36), residues: 200 loop : -1.46 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 187 HIS 0.007 0.001 HIS A 992 PHE 0.027 0.001 PHE A1125 TYR 0.014 0.001 TYR A1360 ARG 0.007 0.000 ARG F 199 Details of bonding type rmsd link_NAG-ASN : bond 0.01073 ( 12) link_NAG-ASN : angle 5.75244 ( 36) link_BETA1-4 : bond 0.00435 ( 10) link_BETA1-4 : angle 1.87148 ( 30) hydrogen bonds : bond 0.04090 ( 946) hydrogen bonds : angle 4.20675 ( 2738) SS BOND : bond 0.00248 ( 13) SS BOND : angle 1.23019 ( 26) covalent geometry : bond 0.00409 (18871) covalent geometry : angle 0.58264 (25605) *********************** 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 304 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 239 time to evaluate : 2.024 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: A 493 MET cc_start: 0.6396 (ptt) cc_final: 0.5275 (mtt) REVERT: A 666 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: A 894 LYS cc_start: 0.6278 (mmmt) cc_final: 0.5303 (mttp) REVERT: A 983 MET cc_start: 0.8775 (mtp) cc_final: 0.8556 (mtm) REVERT: A 1243 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8030 (pt) REVERT: A 1429 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6033 (mp) REVERT: E 53 LEU cc_start: 0.7286 (mm) cc_final: 0.7010 (mp) REVERT: E 127 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8022 (mtt) REVERT: E 165 MET cc_start: 0.4712 (OUTLIER) cc_final: 0.3386 (tpt) REVERT: F 546 ARG cc_start: 0.7680 (tpp-160) cc_final: 0.6986 (tpt170) REVERT: F 603 ASP cc_start: 0.8579 (m-30) cc_final: 0.8128 (m-30) REVERT: F 977 CYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8730 (p) REVERT: F 997 LEU cc_start: 0.7591 (pt) cc_final: 0.7316 (tp) outliers start: 65 outliers final: 31 residues processed: 274 average time/residue: 0.9673 time to fit residues: 309.1522 Evaluate side-chains 268 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 2.067 ------------------------------------------------------------------------------- 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 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 291 MET 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 514 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 578 MET 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 1056 MET Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 151 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 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 Chi-restraints excluded: chain F residue 994 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 154 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.158731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113230 restraints weight = 32371.843| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.71 r_work: 0.3056 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 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 = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18906 Z= 0.121 Angle : 0.597 19.244 25697 Z= 0.288 Chirality : 0.044 0.397 2952 Planarity : 0.004 0.046 3192 Dihedral : 6.080 55.658 2999 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.52 % Allowed : 17.84 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2212 helix: 1.90 (0.15), residues: 1117 sheet: 0.15 (0.36), residues: 200 loop : -1.37 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 187 HIS 0.003 0.001 HIS A 992 PHE 0.030 0.001 PHE F1006 TYR 0.013 0.001 TYR A 834 ARG 0.006 0.000 ARG F 199 Details of bonding type rmsd link_NAG-ASN : bond 0.01245 ( 12) link_NAG-ASN : angle 5.70456 ( 36) link_BETA1-4 : bond 0.00434 ( 10) link_BETA1-4 : angle 1.77353 ( 30) hydrogen bonds : bond 0.03706 ( 946) hydrogen bonds : angle 4.10675 ( 2738) SS BOND : bond 0.00230 ( 13) SS BOND : angle 0.97393 ( 26) covalent geometry : bond 0.00274 (18871) covalent geometry : angle 0.55468 (25605) *********************** 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 286 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: A 493 MET cc_start: 0.6501 (ptt) cc_final: 0.5305 (mtt) REVERT: A 666 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: A 668 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6466 (pp20) REVERT: A 894 LYS cc_start: 0.6124 (mmmt) cc_final: 0.5158 (mttp) REVERT: A 983 MET cc_start: 0.8800 (mtp) cc_final: 0.8512 (mtt) REVERT: A 1243 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7962 (pt) REVERT: A 1429 ILE cc_start: 0.6500 (OUTLIER) cc_final: 0.5949 (mp) REVERT: E 53 LEU cc_start: 0.7502 (mm) cc_final: 0.7235 (mp) REVERT: E 127 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8017 (mtt) REVERT: E 142 MET cc_start: 0.8551 (mpp) cc_final: 0.8245 (mmm) REVERT: E 165 MET cc_start: 0.4643 (OUTLIER) cc_final: 0.3087 (tpt) REVERT: F 55 HIS cc_start: 0.7628 (m90) cc_final: 0.7417 (m90) REVERT: F 546 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7031 (tpt170) REVERT: F 584 GLU cc_start: 0.7832 (tt0) cc_final: 0.7600 (mt-10) REVERT: F 594 VAL cc_start: 0.9168 (t) cc_final: 0.8846 (m) REVERT: F 603 ASP cc_start: 0.8675 (m-30) cc_final: 0.8175 (m-30) REVERT: F 977 CYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8875 (p) outliers start: 50 outliers final: 30 residues processed: 262 average time/residue: 1.0955 time to fit residues: 332.5809 Evaluate side-chains 265 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 2.378 ------------------------------------------------------------------------------- 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 260 GLU Chi-restraints excluded: chain A residue 289 ILE 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 543 THR Chi-restraints excluded: chain A residue 578 MET 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 876 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1059 ILE 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 1332 CYS Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 151 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 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 Chi-restraints excluded: chain F residue 994 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 182 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 221 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.157994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112876 restraints weight = 36927.249| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.61 r_work: 0.3056 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 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 = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18906 Z= 0.116 Angle : 0.602 19.118 25697 Z= 0.289 Chirality : 0.043 0.395 2952 Planarity : 0.004 0.048 3192 Dihedral : 6.021 55.724 2999 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.32 % Allowed : 18.35 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2212 helix: 1.95 (0.15), residues: 1117 sheet: 0.16 (0.36), residues: 200 loop : -1.34 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.003 0.001 HIS A 992 PHE 0.028 0.001 PHE A1125 TYR 0.018 0.001 TYR A 834 ARG 0.008 0.000 ARG F 199 Details of bonding type rmsd link_NAG-ASN : bond 0.01147 ( 12) link_NAG-ASN : angle 5.66751 ( 36) link_BETA1-4 : bond 0.00445 ( 10) link_BETA1-4 : angle 1.75100 ( 30) hydrogen bonds : bond 0.03640 ( 946) hydrogen bonds : angle 4.08775 ( 2738) SS BOND : bond 0.00226 ( 13) SS BOND : angle 0.92687 ( 26) covalent geometry : bond 0.00260 (18871) covalent geometry : angle 0.56049 (25605) *********************** 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 282 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 1.916 Fit side-chains revert: symmetry clash REVERT: A 493 MET cc_start: 0.6484 (ptt) cc_final: 0.5284 (mtt) REVERT: A 666 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: A 668 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6517 (pp20) REVERT: A 894 LYS cc_start: 0.6083 (mmmt) cc_final: 0.5122 (mttp) REVERT: A 983 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8548 (mtt) REVERT: A 1243 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8006 (pt) REVERT: A 1429 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.5992 (mp) REVERT: E 53 LEU cc_start: 0.7485 (mm) cc_final: 0.7114 (mm) REVERT: E 127 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8031 (mtt) REVERT: E 142 MET cc_start: 0.8574 (mpp) cc_final: 0.8284 (mmm) REVERT: E 165 MET cc_start: 0.4792 (OUTLIER) cc_final: 0.3402 (tpt) REVERT: F 55 HIS cc_start: 0.7649 (m90) cc_final: 0.7432 (m90) REVERT: F 546 ARG cc_start: 0.7583 (tpp-160) cc_final: 0.7098 (tpt170) REVERT: F 584 GLU cc_start: 0.7826 (tt0) cc_final: 0.7561 (mt-10) REVERT: F 594 VAL cc_start: 0.9178 (t) cc_final: 0.8882 (m) REVERT: F 603 ASP cc_start: 0.8694 (m-30) cc_final: 0.8222 (m-30) REVERT: F 882 ASP cc_start: 0.8666 (t0) cc_final: 0.8214 (t0) REVERT: F 977 CYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8764 (p) outliers start: 46 outliers final: 29 residues processed: 259 average time/residue: 1.2633 time to fit residues: 385.3457 Evaluate side-chains 268 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 2.297 ------------------------------------------------------------------------------- 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 578 MET 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 1059 ILE 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 1332 CYS Chi-restraints excluded: chain A residue 1383 ASN Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 151 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 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 749 LYS Chi-restraints excluded: chain F residue 869 ASP 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 210 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113380 restraints weight = 34785.062| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.72 r_work: 0.3053 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 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 = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.179 18906 Z= 0.149 Angle : 0.603 19.118 25697 Z= 0.290 Chirality : 0.043 0.395 2952 Planarity : 0.004 0.048 3192 Dihedral : 6.047 55.724 2999 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.76 % Allowed : 18.95 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2212 helix: 1.95 (0.15), residues: 1117 sheet: 0.16 (0.36), residues: 200 loop : -1.34 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.003 0.001 HIS A 992 PHE 0.028 0.001 PHE A1125 TYR 0.018 0.001 TYR A 834 ARG 0.008 0.000 ARG F 199 Details of bonding type rmsd link_NAG-ASN : bond 0.01147 ( 12) link_NAG-ASN : angle 5.66751 ( 36) link_BETA1-4 : bond 0.00445 ( 10) link_BETA1-4 : angle 1.75094 ( 30) hydrogen bonds : bond 0.03640 ( 946) hydrogen bonds : angle 4.08775 ( 2738) SS BOND : bond 0.00226 ( 13) SS BOND : angle 0.92684 ( 26) covalent geometry : bond 0.00291 (18871) covalent geometry : angle 0.56133 (25605) *********************** 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 267 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 1.894 Fit side-chains revert: symmetry clash REVERT: A 493 MET cc_start: 0.6474 (ptt) cc_final: 0.5282 (mtt) REVERT: A 666 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: A 668 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6528 (pp20) REVERT: A 894 LYS cc_start: 0.6104 (mmmt) cc_final: 0.5139 (mttp) REVERT: A 983 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8551 (mtt) REVERT: A 1243 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8007 (pt) REVERT: A 1429 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6016 (mp) REVERT: E 53 LEU cc_start: 0.7472 (mm) cc_final: 0.7109 (mm) REVERT: E 127 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8051 (mtt) REVERT: E 142 MET cc_start: 0.8574 (mpp) cc_final: 0.8285 (mmm) REVERT: E 165 MET cc_start: 0.4826 (OUTLIER) cc_final: 0.3421 (tpt) REVERT: F 55 HIS cc_start: 0.7697 (m90) cc_final: 0.7481 (m90) REVERT: F 546 ARG cc_start: 0.7605 (tpp-160) cc_final: 0.7117 (tpt170) REVERT: F 584 GLU cc_start: 0.7856 (tt0) cc_final: 0.7574 (mt-10) REVERT: F 594 VAL cc_start: 0.9177 (t) cc_final: 0.8878 (m) REVERT: F 603 ASP cc_start: 0.8674 (m-30) cc_final: 0.8201 (m-30) REVERT: F 882 ASP cc_start: 0.8671 (t0) cc_final: 0.8217 (t0) REVERT: F 977 CYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8794 (p) outliers start: 35 outliers final: 29 residues processed: 248 average time/residue: 0.9997 time to fit residues: 289.3386 Evaluate side-chains 267 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 578 MET 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 1059 ILE 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 1332 CYS Chi-restraints excluded: chain A residue 1383 ASN Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 151 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 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 749 LYS Chi-restraints excluded: chain F residue 869 ASP 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 211 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112584 restraints weight = 40383.662| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.95 r_work: 0.3032 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.177 18906 Z= 0.148 Angle : 0.603 19.118 25697 Z= 0.290 Chirality : 0.043 0.395 2952 Planarity : 0.004 0.048 3192 Dihedral : 6.108 55.725 2999 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.76 % Allowed : 18.95 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2212 helix: 1.95 (0.15), residues: 1117 sheet: 0.16 (0.36), residues: 200 loop : -1.34 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.003 0.001 HIS A 992 PHE 0.028 0.001 PHE A1125 TYR 0.018 0.001 TYR A 834 ARG 0.008 0.000 ARG F 199 Details of bonding type rmsd link_NAG-ASN : bond 0.01147 ( 12) link_NAG-ASN : angle 5.66752 ( 36) link_BETA1-4 : bond 0.00443 ( 10) link_BETA1-4 : angle 1.75077 ( 30) hydrogen bonds : bond 0.03640 ( 946) hydrogen bonds : angle 4.08773 ( 2738) SS BOND : bond 0.00226 ( 13) SS BOND : angle 0.92672 ( 26) covalent geometry : bond 0.00290 (18871) covalent geometry : angle 0.56118 (25605) ********************** 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 266 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 2.013 Fit side-chains revert: symmetry clash REVERT: A 493 MET cc_start: 0.6417 (ptt) cc_final: 0.5241 (mtt) REVERT: A 666 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7166 (tp30) REVERT: A 668 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6503 (pp20) REVERT: A 894 LYS cc_start: 0.6123 (mmmt) cc_final: 0.5157 (mttp) REVERT: A 983 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8433 (mtt) REVERT: A 1243 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7970 (pt) REVERT: A 1429 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.5980 (mp) REVERT: E 53 LEU cc_start: 0.7471 (mm) cc_final: 0.7113 (mm) REVERT: E 127 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8005 (mtt) REVERT: E 142 MET cc_start: 0.8487 (mpp) cc_final: 0.8170 (mmm) REVERT: E 165 MET cc_start: 0.4769 (OUTLIER) cc_final: 0.3414 (tpt) REVERT: F 55 HIS cc_start: 0.7552 (m90) cc_final: 0.7332 (m90) REVERT: F 546 ARG cc_start: 0.7467 (tpp-160) cc_final: 0.7034 (tpt170) REVERT: F 594 VAL cc_start: 0.9115 (t) cc_final: 0.8806 (m) REVERT: F 603 ASP cc_start: 0.8446 (m-30) cc_final: 0.7966 (m-30) REVERT: F 882 ASP cc_start: 0.8597 (t0) cc_final: 0.8124 (t0) REVERT: F 977 CYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8341 (p) outliers start: 35 outliers final: 28 residues processed: 247 average time/residue: 1.0053 time to fit residues: 288.8334 Evaluate side-chains 265 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 578 MET 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 1059 ILE 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 1332 CYS Chi-restraints excluded: chain A residue 1383 ASN Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 151 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 270 THR Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 749 LYS 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 193 optimal weight: 2.9990 chunk 195 optimal weight: 0.0020 chunk 13 optimal weight: 0.0970 chunk 102 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.159019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112665 restraints weight = 39394.144| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.91 r_work: 0.3047 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 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 = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 18906 Z= 0.138 Angle : 0.601 19.116 25697 Z= 0.289 Chirality : 0.043 0.395 2952 Planarity : 0.004 0.047 3192 Dihedral : 6.108 55.724 2999 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.76 % Allowed : 18.95 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2212 helix: 1.95 (0.15), residues: 1117 sheet: 0.16 (0.36), residues: 200 loop : -1.34 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.003 0.001 HIS A 992 PHE 0.027 0.001 PHE A1125 TYR 0.018 0.001 TYR A 834 ARG 0.008 0.000 ARG F 199 Details of bonding type rmsd link_NAG-ASN : bond 0.01148 ( 12) link_NAG-ASN : angle 5.66730 ( 36) link_BETA1-4 : bond 0.00423 ( 10) link_BETA1-4 : angle 1.74816 ( 30) hydrogen bonds : bond 0.03639 ( 946) hydrogen bonds : angle 4.08781 ( 2738) SS BOND : bond 0.00225 ( 13) SS BOND : angle 0.92504 ( 26) covalent geometry : bond 0.00280 (18871) covalent geometry : angle 0.55985 (25605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15329.66 seconds wall clock time: 264 minutes 42.20 seconds (15882.20 seconds total)