Starting phenix.real_space_refine on Tue May 20 16:06:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eog_28375/05_2025/8eog_28375.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eog_28375/05_2025/8eog_28375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eog_28375/05_2025/8eog_28375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eog_28375/05_2025/8eog_28375.map" model { file = "/net/cci-nas-00/data/ceres_data/8eog_28375/05_2025/8eog_28375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eog_28375/05_2025/8eog_28375.cif" } resolution = 3.3 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= -0.061 sd= 0.915 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 Ca 3 9.91 5 P 2 5.49 5 S 106 5.16 5 Na 1 4.78 5 C 12776 2.51 5 N 3236 2.21 5 O 3605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19729 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 7630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7630 Classifications: {'peptide': 955} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 912} Chain breaks: 4 Chain: "K" Number of atoms: 10230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 10230 Classifications: {'peptide': 1270} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1227} Chain breaks: 4 Chain: "C" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 181} Chain: "A" 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: "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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {' CA': 1, ' NA': 1, 'NAG': 5} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 172 Unusual residues: {' CA': 2, 'CLR': 3, 'WNZ': 1, 'WO9': 1} Classifications: {'undetermined': 7, 'water': 3} Link IDs: {None: 9} Time building chain proxies: 11.30, per 1000 atoms: 0.57 Number of scatterers: 19729 At special positions: 0 Unit cell: (132.916, 142.229, 199.798, 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) Ca 3 19.99 S 106 16.00 P 2 15.00 Na 1 11.00 O 3605 8.00 N 3236 7.00 C 12776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 305 " - pdb=" SG CYS D1046 " distance=2.03 Simple disulfide: pdb=" SG CYS D 356 " - pdb=" SG CYS D1061 " distance=2.03 Simple disulfide: pdb=" SG CYS D 406 " - pdb=" SG CYS D1073 " distance=2.03 Simple disulfide: pdb=" SG CYS D 669 " - pdb=" SG CYS D 699 " distance=2.03 Simple disulfide: pdb=" SG CYS D 906 " - pdb=" SG CYS D 976 " distance=2.03 Simple disulfide: pdb=" SG CYS D 998 " - pdb=" SG CYS D1028 " distance=2.03 Simple disulfide: pdb=" SG CYS D1001 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS K 316 " - pdb=" SG CYS K 332 " distance=2.03 Simple disulfide: pdb=" SG CYS K1058 " - pdb=" SG CYS K1069 " distance=2.03 Simple disulfide: pdb=" SG CYS K1431 " - pdb=" SG CYS K1447 " 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 A 1 " - " NAG A 2 " " NAG A 2 " - " NAG A 3 " " NAG B 1 " - " NAG B 2 " " NAG E 1 " - " NAG E 2 " Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 2.3 seconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 16 sheets defined 53.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'D' and resid 31 through 55 removed outlier: 3.729A pdb=" N ILE D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 67 removed outlier: 3.799A pdb=" N ASP D 61 " --> pdb=" O HIS D 57 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR D 66 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 112 removed outlier: 3.772A pdb=" N ALA D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 191 through 202 Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 243 through 251 removed outlier: 4.234A pdb=" N GLY D 249 " --> pdb=" O TRP D 245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D 251 " --> pdb=" O ILE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.612A pdb=" N SER D 267 " --> pdb=" O GLY D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 283 removed outlier: 3.647A pdb=" N LYS D 272 " --> pdb=" O GLY D 268 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 283 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 325 Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.678A pdb=" N GLY D 338 " --> pdb=" O ASP D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 379 removed outlier: 3.727A pdb=" N PHE D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 408 removed outlier: 3.694A pdb=" N ASN D 408 " --> pdb=" O MET D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 425 removed outlier: 3.789A pdb=" N ILE D 421 " --> pdb=" O SER D 417 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE D 423 " --> pdb=" O GLY D 419 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D 425 " --> pdb=" O ILE D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 Processing helix chain 'D' and resid 433 through 440 Processing helix chain 'D' and resid 441 through 444 removed outlier: 3.618A pdb=" N LYS D 444 " --> pdb=" O ASP D 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 441 through 444' Processing helix chain 'D' and resid 481 through 484 removed outlier: 3.591A pdb=" N GLN D 484 " --> pdb=" O LEU D 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 481 through 484' Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 570 through 582 Processing helix chain 'D' and resid 626 through 629 Processing helix chain 'D' and resid 639 through 650 removed outlier: 3.901A pdb=" N LEU D 650 " --> pdb=" O TYR D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 700 through 721 removed outlier: 3.562A pdb=" N ILE D 704 " --> pdb=" O ASN D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 removed outlier: 3.931A pdb=" N GLU D 752 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 762 Processing helix chain 'D' and resid 763 through 772 Processing helix chain 'D' and resid 819 through 829 removed outlier: 3.536A pdb=" N TRP D 823 " --> pdb=" O ASP D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 872 Processing helix chain 'D' and resid 876 through 880 Processing helix chain 'D' and resid 881 through 891 Processing helix chain 'D' and resid 1044 through 1049 removed outlier: 3.559A pdb=" N MET D1048 " --> pdb=" O ASP D1044 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D1049 " --> pdb=" O PRO D1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1044 through 1049' Processing helix chain 'K' and resid 113 through 121 removed outlier: 3.609A pdb=" N VAL K 121 " --> pdb=" O CYS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 144 removed outlier: 4.041A pdb=" N GLU K 127 " --> pdb=" O TRP K 123 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 182 removed outlier: 3.694A pdb=" N TYR K 164 " --> pdb=" O GLU K 160 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 209 removed outlier: 3.802A pdb=" N VAL K 205 " --> pdb=" O ILE K 201 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY K 206 " --> pdb=" O ILE K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 241 Processing helix chain 'K' and resid 242 through 251 removed outlier: 3.961A pdb=" N ARG K 246 " --> pdb=" O LEU K 242 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU K 247 " --> pdb=" O ARG K 243 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL K 248 " --> pdb=" O PRO K 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER K 249 " --> pdb=" O LEU K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 266 removed outlier: 3.579A pdb=" N VAL K 266 " --> pdb=" O ILE K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 290 removed outlier: 3.671A pdb=" N VAL K 275 " --> pdb=" O ILE K 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU K 276 " --> pdb=" O ALA K 272 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE K 290 " --> pdb=" O GLY K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 361 removed outlier: 3.522A pdb=" N THR K 361 " --> pdb=" O PHE K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 377 removed outlier: 3.697A pdb=" N VAL K 368 " --> pdb=" O GLY K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 413 removed outlier: 4.456A pdb=" N TYR K 384 " --> pdb=" O TRP K 380 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY K 406 " --> pdb=" O GLY K 402 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU K 407 " --> pdb=" O VAL K 403 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE K 408 " --> pdb=" O LEU K 404 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU K 413 " --> pdb=" O SER K 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 440 Processing helix chain 'K' and resid 525 through 542 removed outlier: 3.675A pdb=" N LEU K 539 " --> pdb=" O PHE K 535 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE K 541 " --> pdb=" O ASN K 537 " (cutoff:3.500A) Processing helix chain 'K' and resid 552 through 567 removed outlier: 3.879A pdb=" N ASN K 560 " --> pdb=" O GLN K 556 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA K 565 " --> pdb=" O LYS K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 568 through 577 Processing helix chain 'K' and resid 579 through 584 Processing helix chain 'K' and resid 589 through 594 Processing helix chain 'K' and resid 595 through 609 removed outlier: 3.882A pdb=" N ILE K 604 " --> pdb=" O ILE K 600 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU K 607 " --> pdb=" O THR K 603 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR K 608 " --> pdb=" O ILE K 604 " (cutoff:3.500A) Processing helix chain 'K' and resid 612 through 631 removed outlier: 4.491A pdb=" N LEU K 619 " --> pdb=" O GLY K 615 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS K 629 " --> pdb=" O LEU K 625 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE K 630 " --> pdb=" O ARG K 626 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR K 631 " --> pdb=" O ILE K 627 " (cutoff:3.500A) Processing helix chain 'K' and resid 637 through 673 removed outlier: 3.732A pdb=" N SER K 650 " --> pdb=" O ASN K 646 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N SER K 653 " --> pdb=" O ARG K 649 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU K 654 " --> pdb=" O SER K 650 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 705 removed outlier: 3.507A pdb=" N GLY K 705 " --> pdb=" O GLN K 701 " (cutoff:3.500A) Processing helix chain 'K' and resid 708 through 719 removed outlier: 3.659A pdb=" N TYR K 719 " --> pdb=" O GLY K 715 " (cutoff:3.500A) Processing helix chain 'K' and resid 729 through 763 removed outlier: 4.021A pdb=" N PHE K 733 " --> pdb=" O VAL K 729 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY K 740 " --> pdb=" O LEU K 736 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN K 741 " --> pdb=" O PHE K 737 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA K 750 " --> pdb=" O ASN K 746 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP K 754 " --> pdb=" O ALA K 750 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN K 755 " --> pdb=" O ILE K 751 " (cutoff:3.500A) Processing helix chain 'K' and resid 890 through 898 Processing helix chain 'K' and resid 900 through 917 removed outlier: 3.658A pdb=" N ASN K 904 " --> pdb=" O THR K 900 " (cutoff:3.500A) Processing helix chain 'K' and resid 927 through 951 removed outlier: 4.462A pdb=" N LEU K 933 " --> pdb=" O ARG K 929 " (cutoff:3.500A) Processing helix chain 'K' and resid 967 through 980 removed outlier: 4.226A pdb=" N ILE K 971 " --> pdb=" O ASN K 967 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU K 974 " --> pdb=" O ASN K 970 " (cutoff:3.500A) Processing helix chain 'K' and resid 1002 through 1011 Processing helix chain 'K' and resid 1012 through 1016 removed outlier: 3.725A pdb=" N LEU K1015 " --> pdb=" O ALA K1012 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS K1016 " --> pdb=" O LYS K1013 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1012 through 1016' Processing helix chain 'K' and resid 1019 through 1030 removed outlier: 3.685A pdb=" N VAL K1024 " --> pdb=" O GLN K1020 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA K1025 " --> pdb=" O CYS K1021 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY K1030 " --> pdb=" O ILE K1026 " (cutoff:3.500A) Processing helix chain 'K' and resid 1030 through 1051 removed outlier: 3.692A pdb=" N THR K1036 " --> pdb=" O ILE K1032 " (cutoff:3.500A) Processing helix chain 'K' and resid 1065 through 1069 Processing helix chain 'K' and resid 1104 through 1113 Processing helix chain 'K' and resid 1116 through 1126 removed outlier: 3.704A pdb=" N LEU K1120 " --> pdb=" O GLY K1116 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP K1126 " --> pdb=" O TYR K1122 " (cutoff:3.500A) Processing helix chain 'K' and resid 1139 through 1141 No H-bonds generated for 'chain 'K' and resid 1139 through 1141' Processing helix chain 'K' and resid 1142 through 1158 removed outlier: 4.284A pdb=" N PHE K1146 " --> pdb=" O ILE K1142 " (cutoff:3.500A) Processing helix chain 'K' and resid 1159 through 1171 Processing helix chain 'K' and resid 1183 through 1194 removed outlier: 3.861A pdb=" N GLN K1188 " --> pdb=" O LYS K1184 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR K1192 " --> pdb=" O GLN K1188 " (cutoff:3.500A) Processing helix chain 'K' and resid 1210 through 1215 removed outlier: 3.591A pdb=" N TYR K1214 " --> pdb=" O LYS K1211 " (cutoff:3.500A) Processing helix chain 'K' and resid 1218 through 1236 removed outlier: 4.332A pdb=" N LEU K1224 " --> pdb=" O TYR K1220 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N MET K1225 " --> pdb=" O PHE K1221 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE K1226 " --> pdb=" O GLU K1222 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL K1227 " --> pdb=" O TYR K1223 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU K1230 " --> pdb=" O PHE K1226 " (cutoff:3.500A) Processing helix chain 'K' and resid 1237 through 1239 No H-bonds generated for 'chain 'K' and resid 1237 through 1239' Processing helix chain 'K' and resid 1244 through 1271 Processing helix chain 'K' and resid 1274 through 1279 removed outlier: 4.356A pdb=" N PHE K1279 " --> pdb=" O PRO K1275 " (cutoff:3.500A) Processing helix chain 'K' and resid 1281 through 1301 Processing helix chain 'K' and resid 1326 through 1335 removed outlier: 4.050A pdb=" N LEU K1330 " --> pdb=" O THR K1326 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE K1331 " --> pdb=" O PHE K1327 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG K1332 " --> pdb=" O PHE K1328 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL K1333 " --> pdb=" O ARG K1329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET K1334 " --> pdb=" O LEU K1330 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG K1335 " --> pdb=" O PHE K1331 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1326 through 1335' Processing helix chain 'K' and resid 1336 through 1342 Processing helix chain 'K' and resid 1344 through 1356 Processing helix chain 'K' and resid 1358 through 1382 removed outlier: 4.649A pdb=" N TYR K1362 " --> pdb=" O GLN K1358 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU K1366 " --> pdb=" O TYR K1362 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE K1367 " --> pdb=" O VAL K1363 " (cutoff:3.500A) Processing helix chain 'K' and resid 1401 through 1415 Processing helix chain 'K' and resid 1417 through 1424 Processing helix chain 'K' and resid 1451 through 1478 Processing helix chain 'K' and resid 1478 through 1483 Processing helix chain 'K' and resid 1490 through 1504 removed outlier: 4.216A pdb=" N LEU K1494 " --> pdb=" O GLY K1490 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP K1495 " --> pdb=" O PRO K1491 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU K1496 " --> pdb=" O HIS K1492 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA K1502 " --> pdb=" O LYS K1498 " (cutoff:3.500A) Processing helix chain 'K' and resid 1513 through 1522 removed outlier: 4.943A pdb=" N THR K1519 " --> pdb=" O LEU K1515 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU K1520 " --> pdb=" O ASP K1516 " (cutoff:3.500A) Processing helix chain 'K' and resid 1557 through 1570 removed outlier: 3.554A pdb=" N THR K1561 " --> pdb=" O MET K1557 " (cutoff:3.500A) Processing helix chain 'K' and resid 1577 through 1585 removed outlier: 4.803A pdb=" N GLU K1583 " --> pdb=" O GLU K1579 " (cutoff:3.500A) Processing helix chain 'K' and resid 1586 through 1589 Processing helix chain 'K' and resid 1598 through 1603 removed outlier: 3.812A pdb=" N LEU K1601 " --> pdb=" O MET K1598 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 207 Processing helix chain 'C' and resid 245 through 263 removed outlier: 4.265A pdb=" N GLU C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 removed outlier: 3.925A pdb=" N GLN C 279 " --> pdb=" O HIS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 309 through 314 removed outlier: 4.348A pdb=" N LYS C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 309 through 314' Processing helix chain 'C' and resid 314 through 328 removed outlier: 3.547A pdb=" N GLN C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 360 removed outlier: 3.773A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 70 through 74 Processing sheet with id=AA2, first strand: chain 'D' and resid 124 through 125 removed outlier: 6.111A pdb=" N VAL D 124 " --> pdb=" O GLN D 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 127 through 128 removed outlier: 6.665A pdb=" N TYR D 127 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY D 488 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 492 " --> pdb=" O GLY D 464 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 127 through 128 removed outlier: 6.665A pdb=" N TYR D 127 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY D 488 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 492 " --> pdb=" O GLY D 464 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'D' and resid 300 through 302 removed outlier: 6.535A pdb=" N ILE D 258 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N PHE D 296 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL D 260 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU D 257 " --> pdb=" O MET D 361 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE D 363 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU D 259 " --> pdb=" O PHE D 363 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE D 389 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU D 362 " --> pdb=" O PHE D 389 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL D 391 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR D 364 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N TYR D 413 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR D 388 " --> pdb=" O TYR D 413 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE D 415 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER D 390 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 523 through 525 removed outlier: 6.475A pdb=" N ALA D 516 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 515 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 612 " --> pdb=" O LEU D 621 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 610 " --> pdb=" O LEU D 623 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 540 through 541 removed outlier: 3.637A pdb=" N ILE D 541 " --> pdb=" O GLY D 909 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 660 through 661 removed outlier: 6.652A pdb=" N LYS D 817 " --> pdb=" O LYS D 732 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ARG D 734 " --> pdb=" O GLY D 815 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY D 815 " --> pdb=" O ARG D 734 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N VAL D 736 " --> pdb=" O VAL D 813 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL D 813 " --> pdb=" O VAL D 736 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N THR D 738 " --> pdb=" O PRO D 811 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LYS D 810 " --> pdb=" O ILE D 802 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE D 802 " --> pdb=" O LYS D 810 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA D 812 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET D 795 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 861 through 864 removed outlier: 3.716A pdb=" N MET D 863 " --> pdb=" O ILE D 854 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 855 " --> pdb=" O ILE D1016 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 894 through 906 removed outlier: 3.688A pdb=" N ASN D 897 " --> pdb=" O GLN D 982 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN D 982 " --> pdb=" O ASN D 897 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLN D 903 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N CYS D 976 " --> pdb=" O GLN D 903 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL D 905 " --> pdb=" O GLN D 974 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN D 974 " --> pdb=" O VAL D 905 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D1038 " --> pdb=" O GLU D 979 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 994 through 996 removed outlier: 3.820A pdb=" N GLY D 994 " --> pdb=" O PHE D1005 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE D1005 " --> pdb=" O GLY D 994 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 1057 through 1058 Processing sheet with id=AB5, first strand: chain 'K' and resid 1072 through 1075 Processing sheet with id=AB6, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.530A pdb=" N VAL C 292 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 213 through 216 removed outlier: 6.116A pdb=" N SER C 213 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASP C 270 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR C 215 " --> pdb=" O ASP C 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 902 hydrogen bonds defined for protein. 2550 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: 7.39 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3176 1.31 - 1.44: 5408 1.44 - 1.57: 11399 1.57 - 1.69: 14 1.69 - 1.82: 162 Bond restraints: 20159 Sorted by residual: bond pdb=" C27 WNZ K1704 " pdb=" O26 WNZ K1704 " ideal model delta sigma weight residual 1.329 1.404 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C18 WO9 K1705 " pdb=" O20 WO9 K1705 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C12 WNZ K1704 " pdb=" O14 WNZ K1704 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 NAG D1105 " pdb=" O5 NAG D1105 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C33 WO9 K1705 " pdb=" O32 WO9 K1705 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.00e-02 2.50e+03 9.62e+00 ... (remaining 20154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 27245 4.42 - 8.85: 81 8.85 - 13.27: 5 13.27 - 17.69: 0 17.69 - 22.12: 2 Bond angle restraints: 27333 Sorted by residual: angle pdb=" O20 WNZ K1704 " pdb=" P19 WNZ K1704 " pdb=" O21 WNZ K1704 " ideal model delta sigma weight residual 123.06 100.94 22.12 3.00e+00 1.11e-01 5.43e+01 angle pdb=" O26 WO9 K1705 " pdb=" P25 WO9 K1705 " pdb=" O27 WO9 K1705 " ideal model delta sigma weight residual 122.85 101.27 21.58 3.00e+00 1.11e-01 5.17e+01 angle pdb=" N ARG K 626 " pdb=" CA ARG K 626 " pdb=" C ARG K 626 " ideal model delta sigma weight residual 111.24 104.61 6.63 1.29e+00 6.01e-01 2.64e+01 angle pdb=" N ASN D 183 " pdb=" CA ASN D 183 " pdb=" C ASN D 183 " ideal model delta sigma weight residual 110.80 102.61 8.19 2.13e+00 2.20e-01 1.48e+01 angle pdb=" C LEU D 185 " pdb=" N ASN D 186 " pdb=" CA ASN D 186 " ideal model delta sigma weight residual 120.29 115.01 5.28 1.42e+00 4.96e-01 1.38e+01 ... (remaining 27328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.36: 11177 24.36 - 48.73: 1042 48.73 - 73.09: 157 73.09 - 97.46: 20 97.46 - 121.82: 2 Dihedral angle restraints: 12398 sinusoidal: 5314 harmonic: 7084 Sorted by residual: dihedral pdb=" CB CYS D 906 " pdb=" SG CYS D 906 " pdb=" SG CYS D 976 " pdb=" CB CYS D 976 " ideal model delta sinusoidal sigma weight residual 93.00 163.21 -70.21 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS K1058 " pdb=" SG CYS K1058 " pdb=" SG CYS K1069 " pdb=" CB CYS K1069 " ideal model delta sinusoidal sigma weight residual -86.00 -138.17 52.17 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CB CYS K1431 " pdb=" SG CYS K1431 " pdb=" SG CYS K1447 " pdb=" CB CYS K1447 " ideal model delta sinusoidal sigma weight residual -86.00 -136.42 50.42 1 1.00e+01 1.00e-02 3.48e+01 ... (remaining 12395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2878 0.080 - 0.159: 241 0.159 - 0.239: 6 0.239 - 0.318: 0 0.318 - 0.398: 1 Chirality restraints: 3126 Sorted by residual: chirality pdb=" CB VAL K1081 " pdb=" CA VAL K1081 " pdb=" CG1 VAL K1081 " pdb=" CG2 VAL K1081 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" C2 NAG D1105 " pdb=" C1 NAG D1105 " pdb=" C3 NAG D1105 " pdb=" N2 NAG D1105 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA LEU D 185 " pdb=" N LEU D 185 " pdb=" C LEU D 185 " pdb=" CB LEU D 185 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 3123 not shown) Planarity restraints: 3428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU K 625 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C LEU K 625 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU K 625 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG K 626 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG K 626 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C ARG K 626 " -0.054 2.00e-02 2.50e+03 pdb=" O ARG K 626 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE K 627 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 602 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C GLU K 602 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU K 602 " -0.018 2.00e-02 2.50e+03 pdb=" N THR K 603 " -0.016 2.00e-02 2.50e+03 ... (remaining 3425 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1392 2.73 - 3.28: 20851 3.28 - 3.82: 32073 3.82 - 4.36: 37124 4.36 - 4.90: 62079 Nonbonded interactions: 153519 Sorted by model distance: nonbonded pdb=" O ILE K 600 " pdb=" OG1 THR K 603 " model vdw 2.193 3.040 nonbonded pdb=" OH TYR D 452 " pdb=" OG1 THR D 463 " model vdw 2.210 3.040 nonbonded pdb=" O SER K1094 " pdb=" OG SER K1094 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR D 513 " pdb=" OE2 GLU D 567 " model vdw 2.241 3.040 nonbonded pdb=" O SER D 892 " pdb=" OG SER D 892 " model vdw 2.251 3.040 ... (remaining 153514 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 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.570 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: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 42.710 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.003 0.075 20173 Z= 0.166 Angle : 0.670 22.115 27365 Z= 0.318 Chirality : 0.043 0.398 3126 Planarity : 0.004 0.060 3428 Dihedral : 17.718 121.822 7784 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.52 % Favored : 92.36 % Rotamer: Outliers : 0.56 % Allowed : 29.37 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -1.06 (0.17), residues: 2394 helix: 0.41 (0.16), residues: 1096 sheet: -0.35 (0.37), residues: 223 loop : -2.01 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP K 195 HIS 0.003 0.001 HIS K1493 PHE 0.018 0.001 PHE K 944 TYR 0.012 0.001 TYR D1070 ARG 0.006 0.000 ARG K 418 Details of bonding type rmsd link_BETA1-4 : bond 0.01027 ( 4) link_BETA1-4 : angle 4.75973 ( 12) hydrogen bonds : bond 0.19289 ( 884) hydrogen bonds : angle 7.02076 ( 2550) SS BOND : bond 0.00092 ( 10) SS BOND : angle 0.90629 ( 20) covalent geometry : bond 0.00338 (20159) covalent geometry : angle 0.66220 (27333) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 2.294 Fit side-chains revert: symmetry clash REVERT: D 29 PHE cc_start: 0.5858 (t80) cc_final: 0.5579 (t80) REVERT: D 688 PHE cc_start: 0.8660 (t80) cc_final: 0.8108 (t80) REVERT: K 290 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6171 (p90) REVERT: K 629 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8820 (mmmt) REVERT: K 1238 MET cc_start: 0.6852 (tpp) cc_final: 0.6462 (tpt) REVERT: K 1353 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8332 (t80) REVERT: K 1426 MET cc_start: 0.8327 (mmt) cc_final: 0.7998 (mmt) REVERT: C 196 MET cc_start: 0.7728 (mmt) cc_final: 0.7272 (mmm) outliers start: 12 outliers final: 1 residues processed: 136 average time/residue: 0.3180 time to fit residues: 68.4616 Evaluate side-chains 119 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 629 LYS Chi-restraints excluded: chain K residue 1353 PHE Chi-restraints excluded: chain D residue 1108 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.0030 chunk 182 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** D 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 931 HIS K 935 ASN ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.110231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.073339 restraints weight = 57919.508| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.76 r_work: 0.3011 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20173 Z= 0.139 Angle : 0.607 9.962 27365 Z= 0.311 Chirality : 0.042 0.262 3126 Planarity : 0.004 0.058 3428 Dihedral : 8.060 81.070 3162 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 2.85 % Allowed : 26.47 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -0.61 (0.18), residues: 2394 helix: 0.92 (0.16), residues: 1130 sheet: -0.19 (0.38), residues: 215 loop : -1.99 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 195 HIS 0.003 0.001 HIS K1240 PHE 0.017 0.001 PHE K 628 TYR 0.021 0.001 TYR K1192 ARG 0.007 0.000 ARG D 691 Details of bonding type rmsd link_BETA1-4 : bond 0.01122 ( 4) link_BETA1-4 : angle 4.07458 ( 12) hydrogen bonds : bond 0.05606 ( 884) hydrogen bonds : angle 5.01310 ( 2550) SS BOND : bond 0.00133 ( 10) SS BOND : angle 0.65482 ( 20) covalent geometry : bond 0.00291 (20159) covalent geometry : angle 0.60092 (27333) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 119 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 311 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8536 (tt0) REVERT: D 650 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8819 (mm) REVERT: D 863 MET cc_start: 0.7427 (ttp) cc_final: 0.7118 (tpp) REVERT: K 145 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8770 (tt) REVERT: K 290 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.6952 (p90) REVERT: K 360 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9095 (tt) REVERT: K 410 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8682 (pptt) REVERT: K 629 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8624 (mmmt) REVERT: K 952 MET cc_start: 0.6584 (ppp) cc_final: 0.6139 (mmm) REVERT: K 970 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8452 (t0) REVERT: K 1223 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8048 (t80) REVERT: K 1400 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.6004 (pm20) REVERT: K 1546 MET cc_start: 0.3027 (tpp) cc_final: 0.2751 (tpp) REVERT: C 319 MET cc_start: 0.8799 (pmm) cc_final: 0.8555 (pmm) REVERT: C 320 MET cc_start: 0.8860 (ppp) cc_final: 0.8403 (tpp) outliers start: 61 outliers final: 24 residues processed: 174 average time/residue: 0.2836 time to fit residues: 79.3125 Evaluate side-chains 143 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 769 SER Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain K residue 138 CYS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 410 LYS Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 629 LYS Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 751 ILE Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain K residue 970 ASN Chi-restraints excluded: chain K residue 976 VAL Chi-restraints excluded: chain K residue 992 ASN Chi-restraints excluded: chain K residue 1002 VAL Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1353 PHE Chi-restraints excluded: chain K residue 1400 GLN Chi-restraints excluded: chain K residue 1422 MET Chi-restraints excluded: chain K residue 1475 ILE Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 1108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 22 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** D 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 924 GLN ** K1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.108810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.071971 restraints weight = 57954.800| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.84 r_work: 0.2950 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20173 Z= 0.183 Angle : 0.606 10.899 27365 Z= 0.311 Chirality : 0.043 0.313 3126 Planarity : 0.004 0.054 3428 Dihedral : 7.189 69.020 3162 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.06 % Favored : 92.82 % Rotamer: Outliers : 3.92 % Allowed : 26.38 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -0.61 (0.18), residues: 2394 helix: 0.98 (0.16), residues: 1132 sheet: -0.39 (0.37), residues: 213 loop : -2.03 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 195 HIS 0.004 0.001 HIS D1006 PHE 0.027 0.001 PHE K 395 TYR 0.016 0.001 TYR D 514 ARG 0.006 0.000 ARG K 418 Details of bonding type rmsd link_BETA1-4 : bond 0.01101 ( 4) link_BETA1-4 : angle 4.25106 ( 12) hydrogen bonds : bond 0.05512 ( 884) hydrogen bonds : angle 4.79294 ( 2550) SS BOND : bond 0.00217 ( 10) SS BOND : angle 0.69546 ( 20) covalent geometry : bond 0.00424 (20159) covalent geometry : angle 0.59977 (27333) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 115 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 311 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8657 (tt0) REVERT: D 508 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8362 (mt) REVERT: D 1012 ASN cc_start: 0.9257 (OUTLIER) cc_final: 0.8991 (t0) REVERT: K 145 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8783 (tt) REVERT: K 290 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7245 (p90) REVERT: K 410 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8589 (pptt) REVERT: K 629 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8667 (mmtt) REVERT: K 952 MET cc_start: 0.6843 (ppp) cc_final: 0.6433 (mmm) REVERT: K 1080 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7707 (pp20) REVERT: K 1223 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.7947 (t80) REVERT: K 1399 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6059 (t80) REVERT: K 1400 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6096 (pm20) REVERT: K 1546 MET cc_start: 0.3069 (OUTLIER) cc_final: 0.2774 (tpp) REVERT: C 302 ARG cc_start: 0.8270 (tpm170) cc_final: 0.8056 (tpp-160) outliers start: 84 outliers final: 47 residues processed: 187 average time/residue: 0.3024 time to fit residues: 89.9703 Evaluate side-chains 166 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 107 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 769 SER Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 813 VAL Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 894 TYR Chi-restraints excluded: chain D residue 1012 ASN Chi-restraints excluded: chain K residue 138 CYS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 273 LEU Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 343 ILE Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 410 LYS Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 538 THR Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 629 LYS Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 751 ILE Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 976 VAL Chi-restraints excluded: chain K residue 992 ASN Chi-restraints excluded: chain K residue 1002 VAL Chi-restraints excluded: chain K residue 1003 LEU Chi-restraints excluded: chain K residue 1080 GLU Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1129 THR Chi-restraints excluded: chain K residue 1158 MET Chi-restraints excluded: chain K residue 1160 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1230 LEU Chi-restraints excluded: chain K residue 1353 PHE Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1400 GLN Chi-restraints excluded: chain K residue 1422 MET Chi-restraints excluded: chain K residue 1475 ILE Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain K residue 1546 MET Chi-restraints excluded: chain K residue 1570 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 1108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 186 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 138 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 240 optimal weight: 5.9990 chunk 73 optimal weight: 0.0030 chunk 96 optimal weight: 0.0470 chunk 69 optimal weight: 0.1980 overall best weight: 0.3688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN D 826 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 894 HIS K 924 GLN K1100 ASN ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.111152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.074557 restraints weight = 58027.300| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 4.08 r_work: 0.3023 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20173 Z= 0.111 Angle : 0.566 9.969 27365 Z= 0.284 Chirality : 0.041 0.233 3126 Planarity : 0.004 0.056 3428 Dihedral : 6.650 72.977 3162 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.78 % Rotamer: Outliers : 3.41 % Allowed : 26.84 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -0.39 (0.18), residues: 2394 helix: 1.15 (0.16), residues: 1132 sheet: -0.10 (0.37), residues: 214 loop : -1.95 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 195 HIS 0.002 0.001 HIS K 545 PHE 0.021 0.001 PHE K1161 TYR 0.021 0.001 TYR K 938 ARG 0.007 0.000 ARG K 418 Details of bonding type rmsd link_BETA1-4 : bond 0.01133 ( 4) link_BETA1-4 : angle 3.93910 ( 12) hydrogen bonds : bond 0.04257 ( 884) hydrogen bonds : angle 4.44555 ( 2550) SS BOND : bond 0.00083 ( 10) SS BOND : angle 0.50769 ( 20) covalent geometry : bond 0.00221 (20159) covalent geometry : angle 0.55975 (27333) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 119 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 311 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: D 650 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8803 (mm) REVERT: K 290 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7284 (p90) REVERT: K 410 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8594 (pptt) REVERT: K 952 MET cc_start: 0.6887 (ppp) cc_final: 0.6431 (mmm) REVERT: K 970 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8364 (t0) REVERT: K 1222 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8576 (tm-30) REVERT: K 1223 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8144 (t80) REVERT: K 1226 PHE cc_start: 0.9104 (m-80) cc_final: 0.8512 (m-80) REVERT: K 1400 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.6029 (pm20) REVERT: K 1559 ASN cc_start: 0.5801 (OUTLIER) cc_final: 0.5468 (m-40) REVERT: C 177 MET cc_start: 0.0016 (OUTLIER) cc_final: -0.0430 (ttt) outliers start: 73 outliers final: 38 residues processed: 184 average time/residue: 0.2992 time to fit residues: 87.9676 Evaluate side-chains 159 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 111 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 575 GLU Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 769 SER Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 894 TYR Chi-restraints excluded: chain K residue 208 PHE Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 410 LYS Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 955 TYR Chi-restraints excluded: chain K residue 970 ASN Chi-restraints excluded: chain K residue 992 ASN Chi-restraints excluded: chain K residue 1003 LEU Chi-restraints excluded: chain K residue 1083 HIS Chi-restraints excluded: chain K residue 1106 MET Chi-restraints excluded: chain K residue 1160 ILE Chi-restraints excluded: chain K residue 1222 GLU Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1230 LEU Chi-restraints excluded: chain K residue 1234 ILE Chi-restraints excluded: chain K residue 1346 ILE Chi-restraints excluded: chain K residue 1353 PHE Chi-restraints excluded: chain K residue 1400 GLN Chi-restraints excluded: chain K residue 1422 MET Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain K residue 1559 ASN Chi-restraints excluded: chain K residue 1570 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 264 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 165 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 180 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 HIS D 408 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 924 GLN ** K1400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.110762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.073866 restraints weight = 57909.583| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.98 r_work: 0.3016 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20173 Z= 0.112 Angle : 0.558 10.387 27365 Z= 0.281 Chirality : 0.041 0.230 3126 Planarity : 0.004 0.056 3428 Dihedral : 6.258 70.978 3156 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.56 % Favored : 93.32 % Rotamer: Outliers : 3.73 % Allowed : 26.56 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -0.29 (0.18), residues: 2394 helix: 1.22 (0.16), residues: 1132 sheet: -0.06 (0.39), residues: 201 loop : -1.85 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 195 HIS 0.003 0.001 HIS K1240 PHE 0.027 0.001 PHE K 628 TYR 0.012 0.001 TYR K 384 ARG 0.008 0.000 ARG K 418 Details of bonding type rmsd link_BETA1-4 : bond 0.01126 ( 4) link_BETA1-4 : angle 4.00316 ( 12) hydrogen bonds : bond 0.04150 ( 884) hydrogen bonds : angle 4.32880 ( 2550) SS BOND : bond 0.00098 ( 10) SS BOND : angle 0.49580 ( 20) covalent geometry : bond 0.00240 (20159) covalent geometry : angle 0.55172 (27333) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 118 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 311 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: D 650 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8811 (mm) REVERT: K 290 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7333 (p90) REVERT: K 410 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8555 (pptt) REVERT: K 556 GLN cc_start: 0.5952 (mt0) cc_final: 0.5248 (tt0) REVERT: K 952 MET cc_start: 0.6973 (ppp) cc_final: 0.6398 (mmm) REVERT: K 1070 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8477 (mtpp) REVERT: K 1080 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7684 (pp20) REVERT: K 1222 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8541 (tm-30) REVERT: K 1223 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8178 (t80) REVERT: K 1226 PHE cc_start: 0.9068 (m-80) cc_final: 0.8436 (m-80) REVERT: K 1278 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6870 (t80) REVERT: K 1399 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.5809 (t80) REVERT: K 1559 ASN cc_start: 0.5913 (OUTLIER) cc_final: 0.5607 (m-40) REVERT: C 177 MET cc_start: 0.0058 (OUTLIER) cc_final: -0.0389 (ttt) REVERT: C 196 MET cc_start: 0.7046 (mmt) cc_final: 0.6715 (mmt) REVERT: C 302 ARG cc_start: 0.7708 (tpp-160) cc_final: 0.7480 (tpm170) REVERT: C 318 GLN cc_start: 0.6942 (tp-100) cc_final: 0.6710 (tp-100) outliers start: 80 outliers final: 39 residues processed: 188 average time/residue: 0.2830 time to fit residues: 86.2008 Evaluate side-chains 165 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 575 GLU Chi-restraints excluded: chain D residue 585 SER Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 769 SER Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain K residue 196 ASN Chi-restraints excluded: chain K residue 208 PHE Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 410 LYS Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 955 TYR Chi-restraints excluded: chain K residue 992 ASN Chi-restraints excluded: chain K residue 1070 LYS Chi-restraints excluded: chain K residue 1080 GLU Chi-restraints excluded: chain K residue 1083 HIS Chi-restraints excluded: chain K residue 1106 MET Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1222 GLU Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1230 LEU Chi-restraints excluded: chain K residue 1234 ILE Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1346 ILE Chi-restraints excluded: chain K residue 1353 PHE Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1422 MET Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain K residue 1559 ASN Chi-restraints excluded: chain K residue 1570 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 264 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 117 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 4 optimal weight: 0.0470 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 overall best weight: 2.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN D 678 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.108878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071454 restraints weight = 57928.632| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.91 r_work: 0.2954 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20173 Z= 0.181 Angle : 0.610 11.168 27365 Z= 0.308 Chirality : 0.043 0.218 3126 Planarity : 0.004 0.054 3428 Dihedral : 6.416 70.920 3156 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.31 % Favored : 92.56 % Rotamer: Outliers : 4.48 % Allowed : 25.72 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -0.40 (0.18), residues: 2394 helix: 1.16 (0.16), residues: 1124 sheet: -0.26 (0.39), residues: 189 loop : -1.88 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 440 HIS 0.004 0.001 HIS K 295 PHE 0.030 0.001 PHE K 628 TYR 0.019 0.001 TYR K 938 ARG 0.005 0.000 ARG K 418 Details of bonding type rmsd link_BETA1-4 : bond 0.01086 ( 4) link_BETA1-4 : angle 4.10404 ( 12) hydrogen bonds : bond 0.04929 ( 884) hydrogen bonds : angle 4.45582 ( 2550) SS BOND : bond 0.00205 ( 10) SS BOND : angle 0.58886 ( 20) covalent geometry : bond 0.00422 (20159) covalent geometry : angle 0.60375 (27333) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 113 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 311 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8628 (tt0) REVERT: D 650 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8924 (mm) REVERT: D 1012 ASN cc_start: 0.9261 (OUTLIER) cc_final: 0.8975 (t0) REVERT: K 290 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7177 (p90) REVERT: K 556 GLN cc_start: 0.5983 (mt0) cc_final: 0.5295 (tt0) REVERT: K 952 MET cc_start: 0.6809 (ppp) cc_final: 0.6182 (mmm) REVERT: K 1080 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7740 (pp20) REVERT: K 1081 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8568 (p) REVERT: K 1222 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8517 (tm-30) REVERT: K 1226 PHE cc_start: 0.9145 (m-80) cc_final: 0.8426 (m-80) REVERT: K 1278 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6657 (t80) REVERT: K 1399 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6172 (t80) REVERT: K 1559 ASN cc_start: 0.5768 (OUTLIER) cc_final: 0.5541 (m-40) REVERT: K 1571 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7464 (mmm160) REVERT: C 177 MET cc_start: -0.0184 (OUTLIER) cc_final: -0.0665 (ttt) REVERT: C 302 ARG cc_start: 0.7690 (tpp-160) cc_final: 0.7465 (tpm170) outliers start: 96 outliers final: 55 residues processed: 196 average time/residue: 0.2713 time to fit residues: 86.3418 Evaluate side-chains 179 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 113 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 575 GLU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 769 SER Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 813 VAL Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 1012 ASN Chi-restraints excluded: chain K residue 179 ILE Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 400 VAL Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 410 LYS Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 538 THR Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 545 HIS Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 748 PHE Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 955 TYR Chi-restraints excluded: chain K residue 976 VAL Chi-restraints excluded: chain K residue 992 ASN Chi-restraints excluded: chain K residue 1000 LEU Chi-restraints excluded: chain K residue 1002 VAL Chi-restraints excluded: chain K residue 1080 GLU Chi-restraints excluded: chain K residue 1081 VAL Chi-restraints excluded: chain K residue 1083 HIS Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1160 ILE Chi-restraints excluded: chain K residue 1222 GLU Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1230 LEU Chi-restraints excluded: chain K residue 1234 ILE Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1346 ILE Chi-restraints excluded: chain K residue 1353 PHE Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1422 MET Chi-restraints excluded: chain K residue 1426 MET Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain K residue 1559 ASN Chi-restraints excluded: chain K residue 1570 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 1108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 147 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 146 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** 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 = 0.4058 r_free = 0.4058 target = 0.109302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.072381 restraints weight = 58064.636| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.66 r_work: 0.2980 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20173 Z= 0.146 Angle : 0.609 14.311 27365 Z= 0.301 Chirality : 0.042 0.224 3126 Planarity : 0.004 0.054 3428 Dihedral : 6.360 72.023 3156 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.06 % Favored : 92.86 % Rotamer: Outliers : 3.73 % Allowed : 26.38 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -0.42 (0.18), residues: 2394 helix: 1.14 (0.16), residues: 1129 sheet: -0.26 (0.39), residues: 189 loop : -1.90 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 187 HIS 0.004 0.001 HIS D1006 PHE 0.024 0.001 PHE K 395 TYR 0.015 0.001 TYR K 384 ARG 0.008 0.000 ARG K 418 Details of bonding type rmsd link_BETA1-4 : bond 0.01014 ( 4) link_BETA1-4 : angle 3.98853 ( 12) hydrogen bonds : bond 0.04637 ( 884) hydrogen bonds : angle 4.40412 ( 2550) SS BOND : bond 0.00160 ( 10) SS BOND : angle 0.56322 ( 20) covalent geometry : bond 0.00336 (20159) covalent geometry : angle 0.60307 (27333) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 119 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 311 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8612 (tt0) REVERT: D 650 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8875 (mm) REVERT: D 1008 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: D 1012 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.8998 (t0) REVERT: K 410 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8537 (pptt) REVERT: K 556 GLN cc_start: 0.5979 (mt0) cc_final: 0.5297 (tt0) REVERT: K 572 LEU cc_start: 0.8204 (pp) cc_final: 0.8002 (mm) REVERT: K 952 MET cc_start: 0.6829 (ppp) cc_final: 0.6179 (mmm) REVERT: K 1080 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7744 (pp20) REVERT: K 1081 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8552 (p) REVERT: K 1222 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8517 (tm-30) REVERT: K 1226 PHE cc_start: 0.9124 (m-80) cc_final: 0.8421 (m-80) REVERT: K 1278 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.6868 (t80) REVERT: K 1399 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6314 (t80) REVERT: K 1571 ARG cc_start: 0.7669 (mmm160) cc_final: 0.7423 (mmm160) REVERT: C 177 MET cc_start: -0.0227 (OUTLIER) cc_final: -0.0718 (ttt) REVERT: C 302 ARG cc_start: 0.7693 (tpp-160) cc_final: 0.7461 (tpm170) outliers start: 80 outliers final: 54 residues processed: 186 average time/residue: 0.2818 time to fit residues: 84.7561 Evaluate side-chains 181 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 116 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 575 GLU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 769 SER Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 1008 GLU Chi-restraints excluded: chain D residue 1012 ASN Chi-restraints excluded: chain K residue 138 CYS Chi-restraints excluded: chain K residue 273 LEU Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 400 VAL Chi-restraints excluded: chain K residue 410 LYS Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 751 ILE Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 955 TYR Chi-restraints excluded: chain K residue 976 VAL Chi-restraints excluded: chain K residue 992 ASN Chi-restraints excluded: chain K residue 1000 LEU Chi-restraints excluded: chain K residue 1002 VAL Chi-restraints excluded: chain K residue 1080 GLU Chi-restraints excluded: chain K residue 1081 VAL Chi-restraints excluded: chain K residue 1083 HIS Chi-restraints excluded: chain K residue 1106 MET Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1160 ILE Chi-restraints excluded: chain K residue 1222 GLU Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1230 LEU Chi-restraints excluded: chain K residue 1234 ILE Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1353 PHE Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1422 MET Chi-restraints excluded: chain K residue 1426 MET Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain K residue 1570 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 1108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 214 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1478 ASN K1559 ASN ** K1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.108639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.071724 restraints weight = 58332.126| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.63 r_work: 0.2961 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20173 Z= 0.173 Angle : 0.624 15.845 27365 Z= 0.310 Chirality : 0.043 0.219 3126 Planarity : 0.004 0.053 3428 Dihedral : 6.393 72.149 3156 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.39 % Favored : 92.52 % Rotamer: Outliers : 4.01 % Allowed : 26.19 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -0.49 (0.18), residues: 2394 helix: 1.09 (0.16), residues: 1129 sheet: -0.36 (0.37), residues: 203 loop : -1.95 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 187 HIS 0.004 0.001 HIS D1006 PHE 0.033 0.001 PHE K 395 TYR 0.016 0.001 TYR D 514 ARG 0.006 0.000 ARG K 418 Details of bonding type rmsd link_BETA1-4 : bond 0.01026 ( 4) link_BETA1-4 : angle 4.03314 ( 12) hydrogen bonds : bond 0.04861 ( 884) hydrogen bonds : angle 4.42122 ( 2550) SS BOND : bond 0.00206 ( 10) SS BOND : angle 0.63142 ( 20) covalent geometry : bond 0.00405 (20159) covalent geometry : angle 0.61869 (27333) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 112 time to evaluate : 2.209 Fit side-chains revert: symmetry clash REVERT: D 311 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8629 (tt0) REVERT: D 650 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8899 (mm) REVERT: D 1008 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: K 410 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8534 (pptt) REVERT: K 556 GLN cc_start: 0.6056 (mt0) cc_final: 0.5362 (tt0) REVERT: K 625 LEU cc_start: 0.9280 (mt) cc_final: 0.8918 (tt) REVERT: K 952 MET cc_start: 0.6819 (ppp) cc_final: 0.6137 (mmm) REVERT: K 1080 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7739 (pp20) REVERT: K 1081 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8549 (p) REVERT: K 1222 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8550 (tm-30) REVERT: K 1226 PHE cc_start: 0.9169 (m-80) cc_final: 0.8453 (m-80) REVERT: K 1278 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.6966 (t80) REVERT: K 1399 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6407 (t80) REVERT: K 1571 ARG cc_start: 0.7656 (mmm160) cc_final: 0.7423 (mmm160) REVERT: C 177 MET cc_start: -0.0260 (OUTLIER) cc_final: -0.0763 (ttt) outliers start: 86 outliers final: 58 residues processed: 187 average time/residue: 0.2940 time to fit residues: 88.2073 Evaluate side-chains 181 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 113 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 575 GLU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 769 SER Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 813 VAL Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 1008 GLU Chi-restraints excluded: chain K residue 138 CYS Chi-restraints excluded: chain K residue 273 LEU Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 343 ILE Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 400 VAL Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 410 LYS Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 545 HIS Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 748 PHE Chi-restraints excluded: chain K residue 751 ILE Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 955 TYR Chi-restraints excluded: chain K residue 976 VAL Chi-restraints excluded: chain K residue 992 ASN Chi-restraints excluded: chain K residue 1000 LEU Chi-restraints excluded: chain K residue 1002 VAL Chi-restraints excluded: chain K residue 1080 GLU Chi-restraints excluded: chain K residue 1081 VAL Chi-restraints excluded: chain K residue 1083 HIS Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1160 ILE Chi-restraints excluded: chain K residue 1222 GLU Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1230 LEU Chi-restraints excluded: chain K residue 1234 ILE Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1353 PHE Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1422 MET Chi-restraints excluded: chain K residue 1426 MET Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain K residue 1570 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 1108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.6980 chunk 177 optimal weight: 0.0000 chunk 77 optimal weight: 1.9990 chunk 225 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 3 optimal weight: 0.0770 chunk 30 optimal weight: 0.4980 overall best weight: 0.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** 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 = 0.4082 r_free = 0.4082 target = 0.110797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.073944 restraints weight = 57641.218| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.91 r_work: 0.3013 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20173 Z= 0.110 Angle : 0.603 14.449 27365 Z= 0.293 Chirality : 0.041 0.233 3126 Planarity : 0.004 0.054 3428 Dihedral : 6.041 73.492 3156 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 2.66 % Allowed : 27.64 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -0.35 (0.18), residues: 2394 helix: 1.14 (0.16), residues: 1141 sheet: -0.15 (0.38), residues: 202 loop : -1.86 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 187 HIS 0.002 0.001 HIS D1006 PHE 0.025 0.001 PHE K1161 TYR 0.012 0.001 TYR K 384 ARG 0.008 0.000 ARG K 418 Details of bonding type rmsd link_BETA1-4 : bond 0.01072 ( 4) link_BETA1-4 : angle 3.79509 ( 12) hydrogen bonds : bond 0.03948 ( 884) hydrogen bonds : angle 4.23301 ( 2550) SS BOND : bond 0.00091 ( 10) SS BOND : angle 0.46912 ( 20) covalent geometry : bond 0.00228 (20159) covalent geometry : angle 0.59771 (27333) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 124 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 311 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: D 650 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8845 (mm) REVERT: D 1008 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: K 410 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8490 (pptt) REVERT: K 556 GLN cc_start: 0.6114 (mt0) cc_final: 0.5518 (tt0) REVERT: K 572 LEU cc_start: 0.8176 (pp) cc_final: 0.7964 (mm) REVERT: K 625 LEU cc_start: 0.9269 (mt) cc_final: 0.8927 (tt) REVERT: K 952 MET cc_start: 0.6970 (ppp) cc_final: 0.6254 (mmm) REVERT: K 1080 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7665 (pp20) REVERT: K 1081 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8460 (p) REVERT: K 1222 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: K 1226 PHE cc_start: 0.9112 (m-80) cc_final: 0.8382 (m-80) REVERT: K 1278 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.6909 (t80) REVERT: K 1399 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.6175 (t80) REVERT: K 1524 ILE cc_start: 0.5710 (OUTLIER) cc_final: 0.5083 (tt) REVERT: K 1571 ARG cc_start: 0.7479 (mmm160) cc_final: 0.7243 (mmm160) REVERT: C 177 MET cc_start: 0.0243 (OUTLIER) cc_final: -0.0411 (ttt) REVERT: C 266 LEU cc_start: 0.2118 (OUTLIER) cc_final: 0.1694 (mm) REVERT: C 302 ARG cc_start: 0.6937 (tpt170) cc_final: 0.6726 (tpm170) outliers start: 57 outliers final: 36 residues processed: 174 average time/residue: 0.2886 time to fit residues: 81.1801 Evaluate side-chains 167 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 575 GLU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 769 SER Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 1008 GLU Chi-restraints excluded: chain K residue 273 LEU Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 400 VAL Chi-restraints excluded: chain K residue 410 LYS Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 955 TYR Chi-restraints excluded: chain K residue 992 ASN Chi-restraints excluded: chain K residue 1003 LEU Chi-restraints excluded: chain K residue 1080 GLU Chi-restraints excluded: chain K residue 1081 VAL Chi-restraints excluded: chain K residue 1083 HIS Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1222 GLU Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1230 LEU Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1422 MET Chi-restraints excluded: chain K residue 1426 MET Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain K residue 1524 ILE Chi-restraints excluded: chain K residue 1570 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 16 optimal weight: 0.4980 chunk 228 optimal weight: 0.9990 chunk 224 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** 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 = 0.4079 r_free = 0.4079 target = 0.110593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.073623 restraints weight = 58081.708| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.92 r_work: 0.3010 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20173 Z= 0.113 Angle : 0.605 14.813 27365 Z= 0.295 Chirality : 0.041 0.231 3126 Planarity : 0.004 0.054 3428 Dihedral : 5.847 72.591 3154 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.48 % Rotamer: Outliers : 2.43 % Allowed : 28.24 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -0.31 (0.18), residues: 2394 helix: 1.17 (0.16), residues: 1144 sheet: -0.11 (0.39), residues: 190 loop : -1.84 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 187 HIS 0.003 0.000 HIS D1006 PHE 0.055 0.001 PHE K1563 TYR 0.012 0.001 TYR K 384 ARG 0.006 0.000 ARG K 418 Details of bonding type rmsd link_BETA1-4 : bond 0.01116 ( 4) link_BETA1-4 : angle 3.79003 ( 12) hydrogen bonds : bond 0.03985 ( 884) hydrogen bonds : angle 4.18381 ( 2550) SS BOND : bond 0.00106 ( 10) SS BOND : angle 0.48115 ( 20) covalent geometry : bond 0.00245 (20159) covalent geometry : angle 0.59976 (27333) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 2.221 Fit side-chains revert: symmetry clash REVERT: D 311 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: D 650 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8842 (mm) REVERT: D 1008 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: K 290 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7282 (p90) REVERT: K 556 GLN cc_start: 0.6050 (mt0) cc_final: 0.5469 (tt0) REVERT: K 572 LEU cc_start: 0.8175 (pp) cc_final: 0.7954 (mm) REVERT: K 625 LEU cc_start: 0.9254 (mt) cc_final: 0.8909 (tt) REVERT: K 952 MET cc_start: 0.6967 (ppp) cc_final: 0.6224 (mmm) REVERT: K 1080 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7645 (pp20) REVERT: K 1081 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8489 (p) REVERT: K 1278 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.6874 (t80) REVERT: K 1399 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6169 (t80) REVERT: K 1524 ILE cc_start: 0.5716 (OUTLIER) cc_final: 0.5105 (tt) REVERT: K 1571 ARG cc_start: 0.7416 (mmm160) cc_final: 0.7196 (mmm160) REVERT: C 177 MET cc_start: 0.0179 (OUTLIER) cc_final: -0.0306 (ttt) REVERT: C 302 ARG cc_start: 0.6942 (tpt170) cc_final: 0.6728 (tpm170) outliers start: 52 outliers final: 35 residues processed: 164 average time/residue: 0.2941 time to fit residues: 77.7155 Evaluate side-chains 163 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 575 GLU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 TYR Chi-restraints excluded: chain D residue 769 SER Chi-restraints excluded: chain D residue 813 VAL Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 1008 GLU Chi-restraints excluded: chain K residue 273 LEU Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 553 THR Chi-restraints excluded: chain K residue 633 TYR Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain K residue 953 THR Chi-restraints excluded: chain K residue 955 TYR Chi-restraints excluded: chain K residue 992 ASN Chi-restraints excluded: chain K residue 1080 GLU Chi-restraints excluded: chain K residue 1081 VAL Chi-restraints excluded: chain K residue 1083 HIS Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1230 LEU Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1422 MET Chi-restraints excluded: chain K residue 1426 MET Chi-restraints excluded: chain K residue 1488 ILE Chi-restraints excluded: chain K residue 1524 ILE Chi-restraints excluded: chain K residue 1570 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 43 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 60 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 183 optimal weight: 0.0050 chunk 239 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1580 GLN ** 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 = 0.4083 r_free = 0.4083 target = 0.111068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.074297 restraints weight = 58055.911| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.89 r_work: 0.3021 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 20173 Z= 0.113 Angle : 0.611 14.365 27365 Z= 0.299 Chirality : 0.041 0.232 3126 Planarity : 0.004 0.060 3428 Dihedral : 5.764 72.598 3154 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.44 % Rotamer: Outliers : 2.71 % Allowed : 28.06 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -0.28 (0.18), residues: 2394 helix: 1.19 (0.16), residues: 1145 sheet: -0.02 (0.39), residues: 190 loop : -1.83 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 187 HIS 0.002 0.000 HIS D1006 PHE 0.046 0.001 PHE K1563 TYR 0.012 0.001 TYR K 384 ARG 0.006 0.000 ARG K 418 Details of bonding type rmsd link_BETA1-4 : bond 0.01042 ( 4) link_BETA1-4 : angle 3.74340 ( 12) hydrogen bonds : bond 0.03845 ( 884) hydrogen bonds : angle 4.15864 ( 2550) SS BOND : bond 0.00309 ( 10) SS BOND : angle 1.11762 ( 20) covalent geometry : bond 0.00245 (20159) covalent geometry : angle 0.60578 (27333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12391.09 seconds wall clock time: 214 minutes 36.76 seconds (12876.76 seconds total)